diff --git a/.github/scripts/nftest_coverage_comment.sh b/.github/scripts/nftest_coverage_comment.sh
new file mode 100644
index 00000000..d7949c0f
--- /dev/null
+++ b/.github/scripts/nftest_coverage_comment.sh
@@ -0,0 +1,120 @@
+#!/usr/bin/env bash
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -euo pipefail
+
+FILE=$1
+if [[ ! -s "$FILE" ]]; then
+  echo "Coverage file $FILE is empty. Exiting."
+  exit 1
+fi
+COVERAGE_THRESHOLD=${COVERAGE_THRESHOLD:-90}
+MARKER="<!-- nf-test-coverage-report -->"
+
+: "${GITHUB_TOKEN:?Missing GITHUB_TOKEN}"
+: "${GITHUB_REPOSITORY:?Missing GITHUB_REPOSITORY}"
+: "${GITHUB_EVENT_PATH:?Missing GITHUB_EVENT_PATH}"
+
+# Get PR number
+PR_NUMBER=$(jq -r '.pull_request.number' "$GITHUB_EVENT_PATH")
+
+if [[ -z "$PR_NUMBER" || "$PR_NUMBER" == "null" ]]; then
+  echo "Not running on a pull request. Exiting."
+  exit 0
+fi
+
+# ---- Parse nf-test coverage totals ----
+COVERAGE_LINE=$(grep -E '(COVERAGE:|Status:)' "$FILE" | tail -1 || true)
+if [[ -z "$COVERAGE_LINE" ]]; then
+  echo "ERROR: Could not find coverage line in $FILE"
+  cat "$FILE"
+  exit 1
+fi
+
+if echo "$COVERAGE_LINE" | grep -q 'COVERAGE:'; then
+  TOTAL_COVERAGE=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+(\.[0-9]+)?%' | tr -d '%' || true)
+  HIT_FILES=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+ of' | grep -oE '[0-9]+' || true)
+  TOTAL_FILES=$(echo "$COVERAGE_LINE" | grep -oE 'of [0-9]+' | grep -oE '[0-9]+' || true)
+else
+  # New format: "Status: 26 of 64 modules and workflows are covered ... (40.62%)"
+  TOTAL_COVERAGE=$(echo "$COVERAGE_LINE" | grep -oE '\([0-9]+(\.[0-9]+)?%\)' | tr -d '()%' || true)
+  HIT_FILES=$(echo "$COVERAGE_LINE" | grep -oE '[0-9]+ of' | grep -oE '[0-9]+' || true)
+  TOTAL_FILES=$(echo "$COVERAGE_LINE" | grep -oE 'of [0-9]+' | grep -oE '[0-9]+' || true)
+fi
+
+if [[ -z "$TOTAL_COVERAGE" || \
+    -z "$HIT_FILES" || \
+    -z "$TOTAL_FILES" || "$TOTAL_FILES" -eq 0 ]];
+then
+  echo "Could not parse coverage percentage from: $COVERAGE_LINE"
+  exit 1
+fi
+
+COVERAGE_OK=$(awk -v cov="$TOTAL_COVERAGE" -v th="$COVERAGE_THRESHOLD" \
+  'BEGIN { print (cov >= th) ? "yes" : "no" }')
+
+if [[ "$COVERAGE_OK" == "yes" ]]; then
+  STATUS_ICON="✅"
+  STATUS_TEXT="Coverage meets threshold"
+else
+  STATUS_ICON="❌"
+  STATUS_TEXT="Coverage below ${COVERAGE_THRESHOLD}% threshold"
+fi
+
+
+# ---- Comment body ----
+COMMENT_BODY=$(cat <<EOF
+$MARKER
+### 🧪 nf-test Coverage Report
+
+**Total coverage:** **${TOTAL_COVERAGE}%**  
+**Lines:** $HIT_FILES / $TOTAL_FILES  
+**Status:** $STATUS_ICON $STATUS_TEXT
+EOF
+)
+
+# ---- GitHub API ----
+API_URL="https://api.github.com"
+COMMENTS_URL="$API_URL/repos/$GITHUB_REPOSITORY/issues/$PR_NUMBER/comments"
+AUTH_HEADER="Authorization: Bearer $GITHUB_TOKEN"
+
+EXISTING_COMMENT_ID=$(curl -s \
+  -H "$AUTH_HEADER" \
+  -H "Accept: application/vnd.github+json" \
+  "$COMMENTS_URL" \
+  | jq -r ".[] | select(.body | contains(\"$MARKER\")) | .id")
+
+if [[ -n "$EXISTING_COMMENT_ID" ]]; then
+  echo "Updating existing nf-test coverage comment"
+  curl -s -X PATCH \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$API_URL/repos/$GITHUB_REPOSITORY/issues/comments/$EXISTING_COMMENT_ID" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+else
+  echo "Creating nf-test coverage comment"
+  curl -s -X POST \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$COMMENTS_URL" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+fi
+
+# ---- Fail CI if coverage too low ----
+if [[ "$COVERAGE_OK" != "yes" ]]; then
+  echo "Coverage ${TOTAL_COVERAGE}% is below threshold ${COVERAGE_THRESHOLD}%"
+  exit 1
+fi
diff --git a/.github/scripts/py_coverage_comment.sh b/.github/scripts/py_coverage_comment.sh
new file mode 100644
index 00000000..38404ded
--- /dev/null
+++ b/.github/scripts/py_coverage_comment.sh
@@ -0,0 +1,127 @@
+#!/usr/bin/env bash
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+set -euo pipefail
+
+LCOV_FILE=$1
+if [[ ! -s "$LCOV_FILE" ]]; then
+  echo "Coverage file $LCOV_FILE is empty. Exiting."
+  exit 1
+fi
+COVERAGE_THRESHOLD=${COVERAGE_THRESHOLD:-90}
+MARKER="<!-- python-lcov-coverage-report -->"
+
+: "${GITHUB_TOKEN:?Missing GITHUB_TOKEN}"
+: "${GITHUB_REPOSITORY:?Missing GITHUB_REPOSITORY}"
+: "${GITHUB_EVENT_PATH:?Missing GITHUB_EVENT_PATH}"
+
+# Get PR number
+PR_NUMBER=$(jq -r '.pull_request.number' "$GITHUB_EVENT_PATH")
+
+if [[ -z "$PR_NUMBER" || "$PR_NUMBER" == "null" ]]; then
+  echo "Not running on a pull request. Exiting."
+  exit 0
+fi
+
+# ---- Parse LCOV totals ----
+TOTAL_LINES=$(grep -h '^LF:' "$LCOV_FILE" | awk -F: '{sum += $2} END {print sum}')
+HIT_LINES=$(grep -h '^LH:' "$LCOV_FILE" | awk -F: '{sum += $2} END {print sum}')
+
+if [[ -z "$TOTAL_LINES" || "$TOTAL_LINES" -eq 0 ]]; then
+  echo "Failed to parse LCOV file"
+  exit 1
+fi
+
+TOTAL_COVERAGE=$(awk -v hit="$HIT_LINES" -v total="$TOTAL_LINES" \
+  'BEGIN { printf "%.2f", (hit / total) * 100 }')
+
+COVERAGE_OK=$(awk -v cov="$TOTAL_COVERAGE" -v th="$COVERAGE_THRESHOLD" \
+  'BEGIN { print (cov >= th) ? "yes" : "no" }')
+
+if [[ "$COVERAGE_OK" == "yes" ]]; then
+  STATUS_ICON="✅"
+  STATUS_TEXT="Coverage meets threshold"
+else
+  STATUS_ICON="❌"
+  STATUS_TEXT="Coverage below ${COVERAGE_THRESHOLD}% threshold"
+fi
+
+# ---- Per-file coverage table ----
+TABLE=$(awk '
+BEGIN {
+  print "| File | Coverage |"
+  print "|------|----------|"
+}
+$1 ~ /^SF:/ { file = substr($1,4); lf=0; lh=0 }
+$1 ~ /^LF:/ { lf = substr($1,4) }
+$1 ~ /^LH:/ { lh = substr($1,4) }
+$1 ~ /^end_of_record/ {
+  if (lf > 0) {
+    printf "| %s | %.2f%% |\n", file, (lh / lf) * 100
+  }
+}
+' "$LCOV_FILE")
+
+# ---- Comment body ----
+COMMENT_BODY=$(cat <<EOF
+$MARKER
+### 🐍 Python Coverage Report (coverage.py / lcov)
+
+**Total coverage:** **${TOTAL_COVERAGE}%**  
+**Lines:** $HIT_LINES / $TOTAL_LINES  
+**Status:** $STATUS_ICON $STATUS_TEXT
+
+<details>
+<summary>Per-file coverage</summary>
+
+$TABLE
+
+</details>
+EOF
+)
+
+# ---- GitHub API ----
+API_URL="https://api.github.com"
+COMMENTS_URL="$API_URL/repos/$GITHUB_REPOSITORY/issues/$PR_NUMBER/comments"
+AUTH_HEADER="Authorization: Bearer $GITHUB_TOKEN"
+
+EXISTING_COMMENT_ID=$(curl -s \
+  -H "$AUTH_HEADER" \
+  -H "Accept: application/vnd.github+json" \
+  "$COMMENTS_URL" \
+  | jq -r ".[] | select(.body | contains(\"$MARKER\")) | .id")
+
+if [[ -n "$EXISTING_COMMENT_ID" ]]; then
+  echo "Updating existing Python coverage comment"
+  curl -s -X PATCH \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$API_URL/repos/$GITHUB_REPOSITORY/issues/comments/$EXISTING_COMMENT_ID" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+else
+  echo "Creating Python coverage comment"
+  curl -s -X POST \
+    -H "$AUTH_HEADER" \
+    -H "Accept: application/vnd.github+json" \
+    "$COMMENTS_URL" \
+    -d "$(jq -nc --arg body "$COMMENT_BODY" '{body: $body}')"
+fi
+
+# ---- Fail CI if coverage too low ----
+if [[ "$COVERAGE_OK" != "yes" ]]; then
+  echo "Coverage ${TOTAL_COVERAGE}% is below threshold ${COVERAGE_THRESHOLD}%"
+  exit 1
+fi
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 00000000..c7276650
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,45 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: build
+on: workflow_dispatch
+
+env:
+  PYTHON_SRC_DIR: src/python/ensembl
+  RUST_SRC_DIR: src/rust/ensembl
+  BIN_DIR: nextflow/vcf_prepper/bin
+
+jobs:
+  python:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install/Update Dependencies
+        run: python3 -m pip install --upgrade build
+      - name: Build
+        run: python3 -m build ${{ env.PYTHON_SRC_DIR }}
+
+  rust:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        BUILD_TARGET: [
+          bed_to_wig,
+          merge_bed
+          vcf_to_bed
+        ]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build ${{ matrix.BUILD_TARGET }}
+        run: cargo build --manifest_file ${{ env.RUST_SRC_DIR }}/${{ matrix.BUILD_TARGET }}/Cargo.toml --artifact-dir ${{ BIN_DIR }}
\ No newline at end of file
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
new file mode 100644
index 00000000..465f115a
--- /dev/null
+++ b/.github/workflows/linting.yml
@@ -0,0 +1,47 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+name: linting
+on: workflow_dispatch
+
+# Make sure CI fails on all warnings, including Clippy lints
+env:
+  RUSTFLAGS: "-Dwarnings"
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff Check
+        run: ruff check --output-format=github .
+      - name: Run Ruff Format
+        run: ruff format
+
+  clippy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run Clippy
+        run: cargo clippy --all-targets --all-features
+      - name: Run Rustfmt
+        run: cargo +nightly fmt
\ No newline at end of file
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
deleted file mode 100644
index 6cee70f9..00000000
--- a/.github/workflows/main.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-name: nf-test
-on: [push, pull_request]
-
-jobs:
-  unit-test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: setup
-        run: curl -fsSL https://code.askimed.com/install/nf-test | bash
-      - name: test
-        run: ${GITHUB_WORKSPACE}/nf-test test nextflow/vcf_prepper/tests
diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
new file mode 100644
index 00000000..071d9301
--- /dev/null
+++ b/.github/workflows/unit_test.yml
@@ -0,0 +1,282 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+name: unit-test
+on: [pull_request]
+
+env:
+  ENSEMBL_ROOT_DIR: repos
+
+jobs:
+  check-changes:
+    runs-on: ubuntu-latest
+    outputs:
+      python: ${{ steps.filter.outputs.python }}
+      vcf_prepper: ${{ steps.filter.outputs.vcf_prepper }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            python:
+              - 'src/python/**'
+              - '.github/**'
+            vcf_prepper:
+              - 'nextflow/vcf_prepper/**'
+              - '.github/**'
+
+  python:
+    runs-on: ubuntu-latest
+    needs: check-changes
+    if: needs.check-changes.outputs.python == 'true'
+    defaults:
+      run:
+        shell: bash
+    services:
+      mysql:
+        image: mysql:8.0
+        env:
+          MYSQL_ROOT_PASSWORD: ''
+          MYSQL_ALLOW_EMPTY_PASSWORD: true
+        ports:
+          - 3306:3306
+        options: >-
+          --health-cmd="mysqladmin ping"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=3
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: wait for MySQL
+        run: |
+          while ! mysqladmin ping -h"127.0.0.1" -P3306 --silent; do
+            sleep 1
+          done
+      
+      - name: load databases
+        run: |
+          mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;'
+          mysql -h 127.0.0.1 -u root ensembl_genome_metadata < src/python/tests/variation_utils/data/ensembl_genome_metadata.dump
+          mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;'
+          mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump
+
+      - name: setup Python dependencies
+        run: |
+          python3 -m pip install ${GITHUB_WORKSPACE}/src/python
+
+      - name: pytest
+        run: |
+          pip install pytest coverage
+          coverage run -m pytest ${GITHUB_WORKSPACE}/src/python
+          coverage lcov -o coverage.lcov
+
+      - name: Add coverage reports
+        if: ${{ github.event_name == 'pull_request' }}
+        continue-on-error: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          bash .github/scripts/py_coverage_comment.sh coverage.lcov
+
+
+  vcf_prepper:
+    runs-on: ubuntu-latest
+    needs: check-changes
+    if: needs.check-changes.outputs.vcf_prepper == 'true'
+    defaults:
+      run:
+        shell: bash
+        working-directory: nextflow/vcf_prepper
+    services:
+      mysql:
+        image: mysql:8.0
+        env:
+          MYSQL_ROOT_PASSWORD: ''
+          MYSQL_ALLOW_EMPTY_PASSWORD: true
+        ports:
+          - 3306:3306
+        options: >-
+          --health-cmd="mysqladmin ping"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=3
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/checkout@v4
+        with:
+          repository: Ensembl/ensembl-vep
+          ref: main
+          path: 'nextflow/vcf_prepper/repos/ensembl-vep'
+      - uses: actions/checkout@v4
+        with:
+          repository: Ensembl/ensembl
+          ref: main
+          path: 'nextflow/vcf_prepper/repos/ensembl'
+      - uses: actions/checkout@v4
+        with:
+          repository: Ensembl/ensembl-variation
+          ref: main
+          path: 'nextflow/vcf_prepper/repos/ensembl-variation'
+      - uses: actions/checkout@v4
+        with:
+          repository: Ensembl/VEP_plugins
+          ref: main
+          path: 'nextflow/vcf_prepper/repos/VEP_plugins'
+      - uses: actions/setup-java@v2
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+      - uses: nf-core/setup-nextflow@v1
+        with:
+          version: '24.04.3'
+
+      - name: wait for MySQL
+        run: |
+          while ! mysqladmin ping -h"127.0.0.1" -P3306 --silent; do
+            sleep 1
+          done
+
+      - name: load databases
+        run: |
+          mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;'
+          mysql -h 127.0.0.1 -u root ensembl_genome_metadata < tests/testdata/ensembl_genome_metadata.dump
+          mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;'
+          mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < tests/testdata/homo_sapiens_core_110_38.dump
+
+      - name: setup tools
+        run: |
+          # install pre-requisites
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            zlib1g-dev \
+            libbz2-dev \
+            liblzma-dev \
+            libcurl4-openssl-dev \
+            libssl-dev
+
+          # install htslib
+          HTSLIB_VERSION=1.19
+          wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
+          tar -xjf htslib-${HTSLIB_VERSION}.tar.bz2
+          cd htslib-${HTSLIB_VERSION}
+          
+          ./configure --prefix=/usr/local
+          make -j$(nproc)
+          sudo make install
+
+          # install bcftools
+          BCFTOOLS_VERSION=1.19
+          wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
+          tar -xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2
+          cd bcftools-${BCFTOOLS_VERSION}
+
+          ./configure --prefix=/usr/local
+          make -j$(nproc)
+          sudo make install
+
+          # install ucsc tools
+          wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
+          chmod +x bedToBigBed
+          mv bedToBigBed /usr/local/bin
+          wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
+          chmod +x wigToBigWig
+          mv wigToBigWig /usr/local/bin
+
+          # add to path
+          echo "PATH=/usr/local/bin:$PATH" >> $GITHUB_ENV
+
+      - name: setup nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: setup Python dependencies
+        run: |
+          python3 -m pip install ${GITHUB_WORKSPACE}/src/python
+          python3 -m pip install -r requirements.txt
+
+      - name: setup Perl dependencies
+        run: |
+          BIOPERL_VERSION=release-1-6-924
+          HTSLIB_VERSION=1.19
+          BIOHTS_VERSION=2.11
+          LIB_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos/ensembl-vep/modules/
+
+          # add module path to PERL5LIB
+          for lib_path in ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos/ensembl*/modules 
+          do
+            PERL5LIB=${lib_path}:$PERL5LIB
+          done
+          export PERL5LIB
+
+          # install Module::Build - needed for Bio::DB::HTS
+          sudo apt-get update
+          sudo apt-get install -y cpanminus
+          cpanm Module::Build
+
+          # install Bioperl - needed for Bio::DB::HTS
+          wget https://github.com/bioperl/bioperl-live/archive/$BIOPERL_VERSION.zip
+          unzip $BIOPERL_VERSION.zip
+          rsync -r bioperl-live-$BIOPERL_VERSION/Bio ${LIB_DIR}/
+
+          # install Bio::DB::HTS
+          wget https://github.com/Ensembl/Bio-DB-HTS/archive/$BIOHTS_VERSION.zip
+          unzip $BIOHTS_VERSION.zip
+          cd Bio-DB-HTS-$BIOHTS_VERSION
+          perl Build.PL --htslib ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/htslib-${HTSLIB_VERSION}
+          ./Build
+          rsync -r lib/Bio ${LIB_DIR}/
+          rsync blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so ${LIB_DIR}/
+
+          # add PERL5LIB to env variable
+          echo "PERL5LIB=$PERL5LIB" >> $GITHUB_ENV
+
+      - name: setup Rust dependencies
+        run: |
+          cargo build --manifest-path ${GITHUB_WORKSPACE}/src/rust/ensembl/vcf_to_bed/Cargo.toml
+          cp ${GITHUB_WORKSPACE}/src/rust/ensembl/vcf_to_bed/target/debug/vcf_to_bed \
+            ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/bin/vcf_to_bed
+
+          cargo build --manifest-path ${GITHUB_WORKSPACE}/src/rust/ensembl/bed_to_wig/Cargo.toml
+          cp ${GITHUB_WORKSPACE}/src/rust/ensembl/bed_to_wig/target/debug/bed_to_wig \
+            ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/bin/bed_to_wig
+
+      - name: test
+        run: |
+          export ENSEMBL_ROOT_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/repos
+          export FTP_NFS_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata
+          export OLD_FTP_NFS_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata
+          export PLUGIN_DATA_DIR=${GITHUB_WORKSPACE}/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata
+          
+          sed -i -e 's|\${BASE_DIR}|'"$GITHUB_WORKSPACE"'|g' ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/tests/testdata/input_config.json
+          sed -i -e 's|\${BASE_DIR}|'"$GITHUB_WORKSPACE"'|g' ${GITHUB_WORKSPACE}/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test_vep_config.ini
+          
+          nf-test test . \
+            --coverage \
+            --ci \
+            --profile github | tee nf-test.txt
+
+      - name: Add coverage reports
+        if: ${{ github.event_name == 'pull_request' }}
+        continue-on-error: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          bash ${GITHUB_WORKSPACE}/.github/scripts/nftest_coverage_comment.sh nf-test.txt
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 193c30f0..37c50993 100755
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,28 @@
-**/target
+**/.DS_Store
 **/DEFAULT.ini
+
+# rust target folder
+**/target
+
+# nextflow logs
 **/.nextflow
+**/.nextflow.log*
 **/.nf-test
+**/.nf-test.log*
+
+# python cache, venv, dist
 **/__pycache__
-**/.python-version
\ No newline at end of file
+**/.python-version
+**/venv
+**/dist
+**/.pytest_cache
+
+# folder generated running nf-test
+**/tests/temp
+**/temp
+**/tracks
+**/reports
+**/work
+report.tap
+
+**/.ruff_cache
\ No newline at end of file
diff --git a/README.md b/README.md
index 20735d3e..5556a6bd 100755
--- a/README.md
+++ b/README.md
@@ -1,12 +1,21 @@
 # ensembl-variation-pipelines
 
-nextfow pipelines
-- [vcf_prepper](nextflow/vcf_prepper/README.md)
-
-scripts
-- [create_input_config.py](scripts/create_input_config.py)
-Create input config JSON file as required by vcf_prepper pipeline.
-- [create_metadata_payload.py](scripts/create_metadata_payload.py)
-Create payloads with statistics and variation example for submission to metadata database
-- [create_track_api_metadata.py](scripts/create_track_api_metadata.py)
-Create JSON with metadata about tracks needed for track API
\ No newline at end of file
+## Nextflow Pipelines
+
+- [vcf_prepper](nextflow/vcf_prepper/README.md): Main pipeline for preparing VCF and track data for Ensembl.
+
+## Scripts
+
+The `scripts/` directory contains various utility scripts:
+
+- [auto_create_input_config.py](scripts/auto_create_input_config.py): Automatically generate input config JSON files for vcf_prepper.
+- [calculate_frequency_from_gt.py](scripts/calculate_frequency_from_gt.py): Calculate allele frequency from genotype data. The generated file is used in the population_data.json config file for vcf_prepper.
+- [create_input_config.py](scripts/create_input_config.py): Create input config JSON file as required by vcf_prepper pipeline.
+- [create_metadata_payload.py](scripts/create_metadata_payload.py): Create payloads with statistics and variation examples for submission to metadata database.
+- [create_track_api_metadata.py](scripts/create_track_api_metadata.py): Create JSON with metadata about tracks needed for track API.
+- [preprocess_hgsvc3.py](scripts/preprocess_hgsvc3.py): Convert population data to haplotype format.
+- [test_track_api_endpoint.py](scripts/test_track_api_endpoint.py): Test the track API endpoint after a handover.
+
+## Python Utilities
+
+- [ensembl-variation-utils](src/python/README.md): Python package for pipeline logic, file location, database access, and VEP config generation.
diff --git a/docs/about.md b/docs/about.md
new file mode 100644
index 00000000..2f7bb428
--- /dev/null
+++ b/docs/about.md
@@ -0,0 +1,42 @@
+# . pipeline parameters
+
+
+
+## Generic options
+
+Less common options for the pipeline, typically set in a config file.
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `version` | Display version and exit. | `boolean` | False |  | True |
+
+## Other parameters
+
+| Parameter | Description | Type | Default | Required | Hidden |
+|-----------|-----------|-----------|-----------|-----------|-----------|
+| `release_id` |  | `integer` | 6 |  |  |
+| `repo_dir` |  | `string` | /hps/software/users/ensembl/variation/snhossain |  |  |
+| `input_config` |  | `string` | /Users/snhossain/ensembl-repos/ensembl-variation-pipelines/nextflow/vcf_prepper/assets/input_sources.json |  |  |
+| `ini_file` |  | `string` | /Users/snhossain/ensembl-repos/ensembl-variation-pipelines/nextflow/vcf_prepper/assets/DEFAULT.ini |  |  |
+| `rank_file` |  | `string` | /Users/snhossain/ensembl-repos/ensembl-variation-pipelines/nextflow/vcf_prepper/assets/variation_consequnce_rank.json |  |  |
+| `population_data_file` |  | `string` | None |  |  |
+| `sources_meta_file` |  | `string` | /Users/snhossain/ensembl-repos/ensembl-variation-pipelines/nextflow/vcf_prepper/assets/sources_meta.json |  |  |
+| `cache_dir` |  | `string` | None |  |  |
+| `gff_dir` |  | `string` | None |  |  |
+| `fasta_dir` |  | `string` | None |  |  |
+| `conservation_data_dir` |  | `string` | None |  |  |
+| `output_dir` |  | `string` | /nfs/production/flicek/ensembl/variation/new_website |  |  |
+| `temp_dir` |  | `string` | /nfs/production/flicek/ensembl/variation/new_website/tmp |  |  |
+| `structural_variant` |  | `integer` | 0 |  |  |
+| `use_old_infra` |  | `integer` | 1 |  |  |
+| `use_vep_cache` |  | `integer` | 1 |  |  |
+| `bin_size` |  | `integer` | 250000 |  |  |
+| `remove_nonunique_ids` |  | `integer` | 0 |  |  |
+| `remove_patch_regions` |  | `integer` | 1 |  |  |
+| `skip_vep` |  | `integer` | 0 |  |  |
+| `skip_tracks` |  | `integer` | 0 |  |  |
+| `skip_stats` |  | `integer` | 0 |  |  |
+| `force_create_config` |  | `integer` | 0 |  |  |
+| `rename_clinvar_ids` |  | `integer` | 1 |  |  |
+| `queue_size` |  | `integer` | 1200 |  |  |
+| `queue` |  | `string` | production |  |  |
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..e1dcd229
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,60 @@
+# VCF Prepper
+
+VCF prepper pipeline is an orchestrated way to run VEP. It does the following -
+- process input VCF and format it according to specification
+- generate VEP INI config file
+- run VEP
+
+## Meta-map
+
+Because we extensively use meta-map instead of using more channels to allow extensibility we need to make sure the process that creates/process/generate file and do not set it in the output are set cache to false.
+
+This should be done on file processing that does not take much time so that a pipeline restart is not too castly.
+
+I have tried to not make a complex meta-map and simplify it.
+genome meta will only contain meta regarding genome.
+cache/fasta/gff/plugin/custom_anno each will also contain their own meta.
+
+meta-map will be generated only at the beginning and would not be updated in any of the process. So it will be easier to join/combine channel using genome meta. 
+If we need to use same meta in multiple process and then we need to join/combine it will create problem as the meta would not be considered different.
+
+Before we relied on gff/fasta file name that is fixed and used the meta-map to get their directories. So it was not communicated via the exact process handling the specfic file. Instead of doing that we would rely on file that contain vep config file parts.
+
+## Process name
+
+use PROCESS/PREPARE prefix if the process/workflow update meta-map 
+
+## Project layout
+
+Input config
+- list of genome
+- each genome can have input from multiple source
+
+VEP config
+- generic config; does not specify genome
+- we can create separate config for sv, sv-hgvs3 etc.
+- we can overwrite config for a genome
+- we can not overwrite config for a source in a genome
+
+- the files and params under plugin needs to be list because if there is unkeyed plugin we will need them in order
+
+fasta/gff/cache
+
+if file is provided check if the file exist+valid, if so write that file in output file, otherwise try to process or error
+if dir is provided locate file name using factory, check if the file exists+valid, if so write that file in output file, otherwise try to process or error
+if di/file not provided locate dir+file using factory, process file if needed, if so write that file in output file, otherwise try to process or error
+
+Note:
+if you want to run different vep with different config you better run separate runs of the pipeline
+
+other updates
+- update pipeline so that we can create subworkflow from output of vep run
+    - we can have separate sub-workflow
+
+
+file locator
+file locators locate a file in a particular common storage area - typically FTP or our internal data directory. It can also be another teams data directory or in a hypothetical scenario remote s3 and so on.
+A locator can use a client's help to determine the exact location of a file in that common storage area.
+A storage area can often use different storage media - FTP can use disk and server. We can use a retry mechanism.
+
+Ideally we would like to use fixed locator for a particular file type. For example, FTP loator for GFF, FASTA, etc. So the default will always be 'CURRENT'. We can support a legacy factory until some time and the availability can be checked via a enum type.
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..c17b2e81
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,5 @@
+site_name: MkLorum
+nav:
+  - Home: index.md
+  - About: about.md
+theme: readthedocs
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/Dockerfile b/nextflow/vcf_prepper/Dockerfile
new file mode 100644
index 00000000..51776e54
--- /dev/null
+++ b/nextflow/vcf_prepper/Dockerfile
@@ -0,0 +1,23 @@
+FROM ubuntu:22.04 
+
+LABEL maintainer="ensembl-variation@ebi.ac.uk"
+
+ARG BRANCH_NAME=unit_test
+
+# basic tools
+RUN apt-get update && apt-get -y install \
+    gawk \
+    grep \
+    sed \
+    wget \
+    software-properties-common
+
+# install specific python version from deadsnakes
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update && apt-get -y install python3.7
+
+# install pip and python requirements
+RUN wget https://bootstrap.pypa.io/get-pip.py && python3 get-pip.py
+RUN wget https://raw.githubusercontent.com/nakib103/ensembl-variation-pipelines/$BRANCH_NAME/nextflow/vcf_prepper/requirements.py
+RUN sed -i -e "s/ensembl-variation-pipelines.git@main/ensembl-variation-pipelines.git@$BRANCH_NAME/" requirements.py
+RUN pip install -r requirements.txt
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/LICENSE b/nextflow/vcf_prepper/LICENSE
new file mode 100755
index 00000000..261eeb9e
--- /dev/null
+++ b/nextflow/vcf_prepper/LICENSE
@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
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+      editorial revisions, annotations, elaborations, or other modifications
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+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
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+      Work and such Derivative Works in Source or Object form.
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+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
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+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
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+          include a readable copy of the attribution notices contained
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+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
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+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
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+
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+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
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+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
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+       http://www.apache.org/licenses/LICENSE-2.0
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+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
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diff --git a/nextflow/vcf_prepper/NOTICE b/nextflow/vcf_prepper/NOTICE
new file mode 100755
index 00000000..e254c9ce
--- /dev/null
+++ b/nextflow/vcf_prepper/NOTICE
@@ -0,0 +1,5 @@
+Ensembl
+Copyright [2018-2024] EMBL-European Bioinformatics Institute
+
+This product includes software developed at:
+- EMBL-European Bioinformatics Institute
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/README.md b/nextflow/vcf_prepper/README.md
index ffbeb3ec..1d858162 100755
--- a/nextflow/vcf_prepper/README.md
+++ b/nextflow/vcf_prepper/README.md
@@ -10,6 +10,8 @@ Following repositories are needed for this pipeline -
 
 - `ensembl-variation`
 - `ensembl-vep`
+- `ensembl` 
+- `VEP_plugins`
 
 Make sure you have checked out to correct branch of these repositories.
 
@@ -28,9 +30,11 @@ if [[ -d "$PYENV_ROOT" ]]; then
 fi
 ```
 
-### Rust setup
+### Rust setup (only for development)
 
-These pipeline requires you can run rust executables. There is no Rust environment available in codon. You need to install using your codon user. Run the following command - 
+These pipeline uses some Rust executables. If you want to develop or test those, you need to have Rust installed in your environment. If you just want to run the pipeline, you don't need to worry about Rust setup as the executables are available in the `bin` directory of the repository.
+
+You currently need to install rust environment using your codon user. Run the following command - 
 
 ```
 curl https://sh.rustup.rs -sSf | sh
@@ -45,35 +49,59 @@ module add nextflow-22.10.1-gcc-11.2.0-ju5saqw
 
 nextflow \
 run ${ENSEMBL_ROOT}/ensembl-variation-pipelines/nextflow/vcf_prepper \
-  -profile lsf \
-  --version 110 \
+  -profile slurm \
   --input_config <path/to/input_config.json> \
   --output_dir <path/to/output_dir> \
-  --bin_size 250000 \
-  --remove_nonunique_ids 1 \
-  --remove_patch_regions 1 \
-  --ini_file <path/to/ini_file> \
-  --repo_dir ${repo_dir} \
-  --skip_vep 0 \
-  --skip_tracks 0 \
-  --force_create_config ${force_create_config} \
-  --rename_clinvar_ids 1 \
-  --cache_dir ${cache_dir} \
-  --fasta_dir ${fasta_dir} \
-  --conservation_data_dir ${conservation_data_dir} \
-  --rank_file <path/to/variation_consequnce_rank.json> \
-  -resume
+  --ini_file <path/to/ini_file>
 ```
 
 ## Options
 
-- `version` : (optional) Give the Ensembl version to be used, default: `108`.
 
-Used to get the appropriate Ensembl core database when creating/processing configs.
+### `version` (optional, default: `110`)
+Give the Ensembl version to be used. It is used to get the appropriate Ensembl core database when creating and/or processing configs.
+
+### `release_id` (optional, default: `6`)
+The target release in form of release_id (from metadata database).
+
+### `repo_dir` (mandatory)
+The location of the Ensembl repositories. The pipeline will look for Ensembl repositories such as `ensembl-variation`, `ensembl-vep`, `ensembl`, `VEP_plugins` in this location.
 
-- `input_config` : (optional) Give the full path of the input configuration file, default: `ensembl-variation-pipelines/nextflow/nf_config/input_sources.json`.
+### `output_dir` (optional, default: `launchDir`)
 
-This is a json configuration file containing the source file information. You have to specify the location of VCF files and file type (local or remote). You will also need to give the genome uuid for the species and assembly. The species name is the species_production_name and assembly is the assembly_default value from core database. 
+Give the full path of the dir where the outputs will be generated. By default, it will be the directory from where you are running the pipeline. Make sure you have write access to this directory.
+
+The generated VEP-ed VCF and track files will be stored there. The directory structure would be:
+
+```
+<output_dir>/
+├── api/
+│   ├── <genome uuid 1>/
+│   │   ├── variation.vcf.gz
+│   │   └── variation.vcf.gz.tbi
+│   └── <genome uuid 2>/
+│       ├── variation.vcf.gz
+│       └── variation.vcf.gz.tbi
+└── tracks/
+    ├── <genome uuid 1>/
+    │   ├── variant-dbsnp-details.bb
+    │   ├── variant-dbsnp-summary.bw
+    │   ├── variant-details.bb -> variant-dbsnp-details.bb
+    │   └── variant-details.bb -> variant-dbsnp-details.bb
+    └── <genome uuid 2>/
+        ├── variant-eva-details.bb
+        ├── variant-eva-summary.bw
+        ├── variant-details.bb -> variant-eva-details.bb
+        └── variant-details.bb -> variant-eva-details.bb
+```
+
+### `temp_dir` (optional, default: `launchDir/tmp`)
+Give the full path of the temporary directory to be used by the pipeline. By default, it will be a `tmp` directory inside the output directory. Make sure you have write access to this directory.
+
+### `input_config` (mandatory)
+Give the full path of the input configuration file.
+
+This is a json configuration file containing the input file and related metadata information.
 
 ```
 {
@@ -89,51 +117,120 @@ This is a json configuration file containing the source file information. You ha
   ]
 }
 ```
+- `homo_sapiens_GRCh38`: This should be `<species>_<assembly>` where species is the production_name and assembly is the assembly_default.
 
-- `output_dir` : (optional) Give the full path of the dir where the outputs will be generated, default: `/nfs/production/flicek/ensembl/variation/new_website`
+- `genome_uuid`: We only update the latest partial or (in some rare cases) latest integrated genome. See which one you are updating and make sure to use the correct genome_uuid. It will involve querying the metadata database.
 
-The generated VEP VCF and track files will be stored there. The directory structure would be - 
+- `species`: Use the species production_name value from metadata db from genome table.
 
-```
-<output_dir>
-  |
-  -- api
-      |
-      -- <genome uuid 1>
-          |
-          -- variation.vcf.gz
-          -- variation.vcf.gz.tbi
-      -- <genome uuid 1> 
-          |
-          -- variation.vcf.gz
-          -- variation.vcf.gz.tbi
-      .
-      .
-  -- tracks
-      |
-      -- <genome uuid 1>
-          |
-          -- variant-dbsnp-details.bb
-          -- variant-dbsnp-summary.bw
-          -- variant-details.bb -> variant-dbsnp-details.bb
-          -- variant-details.bb -> variant-dbsnp-details.bb
-      -- <genome uuid 2>
-          |
-          -- variant-eva-details.bb
-          -- variant-eva-summary.bw
-          -- variant-details.bb -> variant-eva-details.bb
-          -- variant-details.bb -> variant-eva-details.bb
-  .
-  .
-```
+- `assembly`: Use the assembly_default value from metadata db from assembly table.
+
+- `source_name`: Specify the name of the source of the VCF file.
+
+- `file_location`: Update with the full path of the source VCF file.
+
+- `file_type`: Specify the type of the source file. It can be `local` or `remote`.
+
+- `sources`: In some special cases where we have multiple sources in a VCF file, we set source_name to `MULTIPLE` and provide the source names in the `sources` field as a list of strings.
+
+### `vep_config` (optional, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/vep_config.json`)
+Give the full path of the VEP configuration file.
 
-- `bin_size` : (optional) This is a nextflow-vep pipeline parameter and determines the number of variants to split the VCF file by, default: `250000`.
+The VEP configuration file must be a JSON file matching the following schema:
 
-- `remove_nonunique_ids` : (optional) If value is 1, the pipeline will ignore duplicate variants with same variant name, default: `1`.
+#### Structure
 
-- `remove_patch_regions` : (optional) If value is 1, the pipeline will ignore sequence region with `PATCH`, `TEST`, `CTG` in name, default: `1`.
+The top-level object contains:
 
-- `ini_file` : (optional) A INI file that is used by the `createConfigs` step to generate the config files, default: `ensembl-variation-pipelines/nextflow/nf_config/DEFAULT.ini`.
+- `annotation_source`: Object describing sources for cache, FASTA, and GFF files.
+  - `cache`: 
+    - `active`: (boolean) specifies if cache is used
+    - `dir`: (string) directory path for cache files
+    - `version`: (integer) cache version
+    - `factory`: (string) factory to use in case we need to fetch and process cache files
+  - `fasta`: 
+    - `active`: (boolean) specifies if FASTA is used
+    - `dir`: (string) directory path for FASTA files, fasta files are expected in this dir
+    - `file`: (string) or, provide full path to the FASTA file
+    - `factory`: (string) factory to use in case we need to fetch and process FASTA files
+  - `gff`: 
+    - `active`: (boolean) specifies if GFF is used
+    - `dir`: (string) directory path for GFF files, GFF files are expected in this dir
+    - `file`: (string) or, provide full path to the GFF file
+    - `factory`: (string) factory to use in case we need to fetch and process GFF files
+- `default_options`: Object specifying default VEP options.
+  - `force_overwrite`, `fork`, `buffer_size`, `vcf`, `spdi`, `variant_class`, `protein`, `transcript_version`, `gencode_promoter`, `offline`, `sift`, `polyphen`, `af_1kg` etc. with their respective values.
+- `plugins`: Object describing plugin configuration.
+  - `genome_matcher`: string, the matcher class to use for matching the genome against avaialble plugins.
+  - `confs`: array of plugin config objects, each with:
+    - `name`: (string) name of the plugin
+    - `requires_file`: (boolean) specifies if the plugin requires a file
+    - `keyed`: (boolean) specifies if the plugin params are keyed
+    - `args`: array of param objects (e.g., `{ key: string }`), replaces any default value generated by the pipeline for the plugin.
+- `custom_annotaions`: Object describing custom annotation configuration.
+  - `confs`: array of custom annotation config objects, each with:
+    - `name`: (string) name of the custom annotation, e.g. - frequency, citation etc.
+    - `genome_matcher`: (string) the matcher class to use for matching the genome against this custom annotation. NOT IMPLEMENTED YET.
+    - `args`: array of param objects (e.g., `{ short_name: string, file: string, format: string, type: string, coord: integer }`), replaces any default value generated by the pipeline for the custom annotation. Currently it will override all custom lines under a certain annotation, e.g. - gnomAD and 1000Genomes frequency.
+
+#### Example
+
+```json
+{
+  "annotation_source": {
+    "cache": { "active": true, "dir": "/path/to/cache", "version": 110, "factory": "old" },
+    "fasta": { "active": true, "dir": "/path/to/fasta", "file": "genome.fa", "factory": "current" },
+    "gff": { "active": false }
+  },
+  "default_options": {
+    "force_overwrite": 1,
+    "fork": 4,
+    "buffer_size": 1000,
+    "vcf": 1,
+    "spdi": 1,
+    "variant_class": 1,
+    "protein": 1,
+    "transcript_version": 1,
+    "gencode_promoter": 1,
+    "offline": 1,
+    "sift": 1,
+    "polyphen": 1,
+    "af_1kg": 1
+  },
+  "plugins": {
+    "confs": [
+      {
+        "name": "PluginA",
+        "requires_file": true,
+        "keyed": false,
+        "files": [{ "snv": "fileA.txt" }],
+        "file_factory": "current",
+        "params": [{ "key": "value" }]
+      }
+    ]
+  },
+  "custom_annotaions": {
+    "confs": [
+      {
+        "name": "CustomA",
+        "file_factory": "current",
+        "params": [
+          {
+            "short_name": "shortA",
+            "file": "customA.txt",
+            "format": "txt",
+            "type": "custom",
+            "coord": 1
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+### `ini_file` (mandatory)
+A INI file that is used by the `createConfigs` step to generate the config files.
 
 The file format is -
 ```
@@ -150,175 +247,227 @@ user = <user>
 
 Add the appropriate server information so that the core database related to the species and Ensembl version can be found.
 
-- `repo_dir` : (optional) the location of the Ensembl repositories, default: `/hps/software/users/ensembl/repositories/${USER}`. 
+### `rank_file` (optional, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/variation_consequnce_rank.json`)
+Give the full path of the rank file to be generated and used.
 
-- `skip_vep` : (optional) If value is 1, the pipeline will skip running `nextflow-vep`, default: `0`. 
-
-If `nextflow-vep` is skipped, the VCF file provided in the `input_config.json` should be VCF files that have already been run through VEP (with appropriate configuration required by vcf_prepper pipeline)
+This rank file contains the rank of variant consequence and used to determine the most severe consequence of a variant. The pipeline generate this file automatically using Ensembl Variation api and later use it in the `vcfToBed` step.
 
-- `skip_tracks` : (optional) If value is 1, the pipeline will skip creating track files. 
+Make sure you are checked out to appropriate `ensembl-variation` repository to get the appropriate ranks. ideally it would be the same version as provided by the `--version` parameter.
 
-- `skip_stats` : (optional) If value is 1, the pipeline will skip updatin api files with stats. 
+### `population_data_file` (optional, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/population_data.json`)
+Give the full path of the population data file to be used.
 
-- `force_create_config` : (optional) If value is 1, the pipeline will forcefully create/process the config files even if they exist, default: `0`.
+### `sources_meta_file` (optional, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/sources_meta.json`)
+Give the full path of the sources meta file to be used.
 
-Config files include - FASTA, Ensembl VEP cache files, Conservation plugin data files, VEP config files, chromosome synonym file, and chromosome size files.
+### `bed_fields` (optional, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/bed_fields.json`)
+Give the full path of the bed fields file to be used.
 
-- `rename_clinvar_ids`: (optional) If value is 1, the pipeline will try to convert id of the ClinVar VCF from ClinVar accession to ClinVar variant ID. 
+### `structural_variant` (optional, default: `0`)
+If value is 1, the pipeline will process structural variant VCFs. If 0, it will treat input file as short variant VCFs.
 
-- `cache_dir` : (optional) Give the full path of the directory where VEP cache should be created if does not exist, default: `/nfs/production/flicek/ensembl/variation/data/VEP/tabixconverted`
+### `bin_size` (optional, default: `250000`)
+This is a nextflow-vep pipeline parameter and determines the number of variants to split the VCF file by.
 
-For human GRCh38 and GRCh37 the default value cannot be overriden using this parameter.
+### `remove_nonunique_ids` (optional, default: `1`)
+If value is 1, the pipeline will ignore duplicate variants with same variant name.
 
-- `fasta_dir` : (optional) Give the full path of the directory where FASTA file should be created if does not exist, default: `/nfs/production/flicek/ensembl/variation/data/VEP/fasta`
+### `remove_patch_regions` (optional, default: `1`)
+If value is 1, the pipeline will ignore sequence region with `PATCH`, `TEST`, `CTG` in name.
 
-For human GRCh38 and GRCh37 the default value cannot be overriden using this parameter.
+### `skip_vep` (optional, default: `0`)
+If value is 1, the pipeline will skip running `nextflow-vep`. If skipped, input VCFs must already be processed by VEP.
 
-- `conservation_data_dir` : (optional) Give the full path of the directory where Conservation plugin data file should be created if does not exist, default: `/nfs/production/flicek/ensembl/variation/data/Conservation`
+### `skip_tracks` (optional, default: `0`)
+If value is 1, the pipeline will skip creating track files.
 
-For human GRCh38 and GRCh37 the default value cannot be overriden using this parameter.
+### `skip_stats` (optional, default: `0`)
+If value is 1, the pipeline will skip updating API files with stats.
 
-- `rank_file` : (optional) Give the full path of the rank file to be generated and used, default: `ensembl-variation-pipelines/nextflow/vcf_prepper/assets/variation_consequnce_rank.json`
+### `rename_clinvar_ids` (optional, default: `1`)
+If value is 1, the pipeline will try to convert id of the ClinVar VCF from ClinVar accession to ClinVar variant ID.
 
-This rank file contains the rank of variant consequence and used to determine the most severe consequence of a variant. The pipeline generate this file automatically using Ensembl Variation api and later use it in the `vcfToBed` step.
+### `queue_size` (optional, default: `1200`)
+This is a nextflow-vep pipeline parameter and determines the number of jobs to be submitted to the cluster at a time.
 
-Make sure you are checked out to appropriate `ensembl-variation` repository to get the appropriate ranks. ideally it would be the same version as provided by the `--version` parameter.
+### `queue` (optional, default: `production`)
+This is a nextflow-vep pipeline parameter and determines the queue to which the jobs will be submitted.
 
 ## Pipeline Flow
 
 ```mermaid
 flowchart TD
-    p0((Channel.fromList))
-    p1(( ))
-    p2[VCF_PREPPER:CREATE_RANK_FILE]
-    p3([map])
-    p4([map])
-    p5([map])
-    p6(( ))
-    p7[VCF_PREPPER:PREPARE_GENOME:GENERATE_SYNONYM_FILE]
-    p8[VCF_PREPPER:PREPARE_GENOME:PROCESS_CACHE]
-    p9[VCF_PREPPER:PREPARE_GENOME:PROCESS_FASTA]
-    p10[VCF_PREPPER:PREPARE_GENOME:PROCESS_CONSERVATION_DATA]
-    p11([map])
-    p12([join])
-    p13([join])
-    p14([join])
-    p15([map])
-    p16[VCF_PREPPER:PREPARE_GENOME:GENERATE_VEP_CONFIG]
-    p17([join])
-    p18[VCF_PREPPER:PREPARE_GENOME:GENERATE_CHROM_SIZES]
-    p19([map])
-    p20([join])
-    p21([join])
-    p22([map])
-    p23[VCF_PREPPER:PREPARE_GENOME:PROCESS_INPUT]
-    p24[VCF_PREPPER:UPDATE_FIELDS]
-    p25[VCF_PREPPER:REMOVE_VARIANTS]
-    p26([map])
-    p27[VCF_PREPPER:RUN_VEP:INDEX_VCF]
-    p28([map])
-    p29[VCF_PREPPER:RUN_VEP:vep:checkVCF]
-    p30(( ))
-    p31[VCF_PREPPER:RUN_VEP:vep:generateSplits]
-    p32([transpose])
-    p33[VCF_PREPPER:RUN_VEP:vep:splitVCF]
-    p34([transpose])
-    p35[VCF_PREPPER:RUN_VEP:vep:runVEP]
-    p36(( ))
-    p37([groupTuple])
-    p38[VCF_PREPPER:RUN_VEP:vep:mergeVCF]
-    p39([map])
-    p40([join])
-    p41([map])
-    p42[VCF_PREPPER:COUNT_VCF_VARIANT]
-    p43([map])
-    p44([filter])
-    p45[VCF_PREPPER:SPLIT_VCF:READ_VCF_CHR]
-    p46([transpose])
-    p47[VCF_PREPPER:SPLIT_VCF:SPLIT_VCF_CHR]
-    p48([transpose])
-    p49[VCF_PREPPER:VCF_TO_BED]
-    p50([groupTuple])
-    p51[VCF_PREPPER:CONCAT_BEDS]
-    p52[VCF_PREPPER:BED_TO_BIGBED]
-    p53(( ))
-    p54[VCF_PREPPER:BED_TO_BIGWIG]
-    p55(( ))
-    p56([map])
-    p57[VCF_PREPPER:SUMMARY_STATS]
-    p58([join])
-    p59([map])
-    p60([map])
-    p61(( ))
-    p0 -->|input| p3
-    p1 -->|rank_file| p2
-    p2 -->|rank_file| p49
-    p3 -->|ch_prepare_genome| p4
-    p4 -->|ch_prepare_genome_meta| p5
-    p5 -->|ch_skip| p6
-    p4 -->|ch_prepare_genome_meta| p7
-    p7 -->|genome| p17
-    p4 -->|ch_prepare_genome_meta| p8
-    p8 -->|genome| p12
-    p4 -->|ch_prepare_genome_meta| p9
-    p9 -->|genome| p13
-    p4 -->|ch_prepare_genome_meta| p10
-    p10 -->|genome| p14
-    p4 -->|ch_prepare_genome_meta| p11
-    p11 --> p12
-    p12 --> p13
-    p13 --> p14
-    p14 --> p15
-    p15 -->|ch_generate_vep_config| p16
-    p16 -->|genome| p17
-    p17 -->|ch_prepared_api| p20
-    p4 -->|ch_prepare_genome_meta| p18
-    p18 -->|genome| p21
-    p3 -->|ch_prepare_genome| p19
-    p19 --> p20
-    p20 --> p21
-    p21 --> p22
-    p22 -->|ch_prepare_source| p23
-    p23 --> p24
-    p24 --> p25
-    p25 -->|input| p26
-    p26 -->|ch_index_vcf| p27
-    p27 --> p28
-    p28 -->|inputs| p29
-    p29 --> p31
-    p30 -->|bin_size| p31
-    p31 --> p32
-    p32 --> p33
-    p33 --> p34
-    p34 --> p35
-    p35 --> p37
-    p35 --> p36
-    p37 --> p38
-    p38 --> p40
-    p25 -->|input| p39
-    p39 --> p40
-    p40 --> p41
-    p41 -->|ch_post_vep| p42
-    p42 --> p43
-    p43 --> p44
-    p44 -->|input| p45
-    p45 --> p46
-    p46 --> p47
-    p47 --> p48
-    p48 --> p49
-    p49 --> p50
-    p50 --> p51
-    p51 --> p52
-    p52 --> p53
-    p51 --> p54
-    p54 --> p55
-    p47 --> p56
-    p56 -->|ch_split_finish| p58
-    p44 -->|input| p57
-    p57 --> p58
-    p58 --> p59
-    p59 -->|ch_post_process| p60
-    p60 --> p61
+    INPUT([input_config.json])
+    VEP_CFG([vep_config.json])
+    INI([ini_file])
+    RANK_IN([rank_file.json])
+
+    subgraph PREPARE_GENOME_SW["PREPARE_GENOME (subworkflow)"]
+        GENERATE_SYNONYM_FILE[GENERATE_SYNONYM_FILE]
+        GENERATE_CHROM_SIZES[GENERATE_CHROM_SIZES]
+    end
+
+    STAGE_VCF[STAGE_VCF]
+
+    subgraph VEP_BLOCK["if not skip_vep"]
+        FORMAT_VCF[FORMAT_VCF]
+        subgraph GENERATE_VEP_CONFIG_SW["GENERATE_VEP_CONFIG (subworkflow)"]
+            direction LR
+            PROCESS_FASTA_CONFIG[PROCESS_FASTA_CONFIG]
+            PROCESS_GFF_CONFIG[PROCESS_GFF_CONFIG]
+            PROCESS_CACHE_CONFIG[PROCESS_CACHE_CONFIG]
+            PROCESS_DEFAULT_OPTIONS_CONFIG[PROCESS_DEFAULT_OPTIONS_CONFIG]
+            PROCESS_PLUGINS_CONFIG[PROCESS_PLUGINS_CONFIG]
+            PROCESS_CUSTOM_ANNOTATIONS_CONFIG[PROCESS_CUSTOM_ANNOTATIONS_CONFIG]
+            CREATE_VEP_CONFIG[CREATE_VEP_CONFIG]
+            PROCESS_FASTA_CONFIG & PROCESS_GFF_CONFIG & PROCESS_CACHE_CONFIG & PROCESS_DEFAULT_OPTIONS_CONFIG & PROCESS_PLUGINS_CONFIG & PROCESS_CUSTOM_ANNOTATIONS_CONFIG --> CREATE_VEP_CONFIG
+        end
+        RUN_VEP["RUN_VEP (subworkflow)\ncheckVCF → splitVCF → runVEP → mergeVCF"]
+        FORMAT_VCF --> RUN_VEP
+        CREATE_VEP_CONFIG --> RUN_VEP
+    end
+
+    COUNT_VCF_VARIANT["COUNT_VCF_VARIANT\n(filter empty VCFs)"]
+
+    subgraph STATS_BLOCK["if not skip_stats"]
+        SUMMARY_STATS[SUMMARY_STATS]
+    end
+
+    subgraph TRACKS_BLOCK["if not skip_tracks"]
+        subgraph SPLIT_VCF_SW["SPLIT_VCF (subworkflow)"]
+            READ_VCF_CHR[READ_VCF_CHR]
+            SPLIT_VCF_CHR[SPLIT_VCF_CHR]
+            READ_VCF_CHR --> SPLIT_VCF_CHR
+        end
+        CREATE_RANK_FILE[CREATE_RANK_FILE]
+        VCF_TO_BED[VCF_TO_BED]
+        CONCAT_BEDS[CONCAT_BEDS]
+        BED_TO_BIGBED[BED_TO_BIGBED]
+        BED_TO_WIG[BED_TO_WIG]
+        WIG_TO_BIGWIG[WIG_TO_BIGWIG]
+        SPLIT_VCF_CHR --> VCF_TO_BED
+        CREATE_RANK_FILE --> VCF_TO_BED
+        VCF_TO_BED --> CONCAT_BEDS
+        CONCAT_BEDS --> BED_TO_BIGBED & BED_TO_WIG
+        BED_TO_WIG --> WIG_TO_BIGWIG
+    end
+
+    API_OUT([api/genome_uuid/variation.vcf.gz])
+    BB_OUT([tracks/genome_uuid/variant-*.bb])
+    BW_OUT([tracks/genome_uuid/variant-*.bw])
+
+    INPUT --> GENERATE_SYNONYM_FILE & GENERATE_CHROM_SIZES
+    INI --> GENERATE_SYNONYM_FILE & GENERATE_CHROM_SIZES
+    INPUT --> STAGE_VCF
+    VEP_CFG --> PROCESS_FASTA_CONFIG & PROCESS_GFF_CONFIG & PROCESS_CACHE_CONFIG & PROCESS_DEFAULT_OPTIONS_CONFIG & PROCESS_PLUGINS_CONFIG & PROCESS_CUSTOM_ANNOTATIONS_CONFIG
+    INI --> PROCESS_FASTA_CONFIG & PROCESS_GFF_CONFIG & PROCESS_CACHE_CONFIG
+    RANK_IN --> CREATE_RANK_FILE
+    GENERATE_SYNONYM_FILE -.->|synonym_file| FORMAT_VCF
+    GENERATE_CHROM_SIZES -.->|chrom_sizes| BED_TO_BIGBED
+    GENERATE_CHROM_SIZES -.->|chrom_sizes| WIG_TO_BIGWIG
+    STAGE_VCF --> FORMAT_VCF
+    STAGE_VCF -.->|skip_vep=1| COUNT_VCF_VARIANT
+    RUN_VEP --> COUNT_VCF_VARIANT
+    COUNT_VCF_VARIANT --> SUMMARY_STATS
+    COUNT_VCF_VARIANT -.->|skip_stats=1| API_OUT
+    COUNT_VCF_VARIANT --> READ_VCF_CHR
+    SUMMARY_STATS --> API_OUT
+    BED_TO_BIGBED --> BB_OUT
+    WIG_TO_BIGWIG --> BW_OUT
+```
+
+## Testing & CI
+
+Unit tests are available for all modules, subworkflows, workflows, and functions. CI runs linting, builds Rust binaries, and builds/tests the Python `ensembl-variation-utils` package.
+
+### Running nf-test locally
+
+#### 1. Replace `BASE_DIR` in test data files
+
+Test data files use `${BASE_DIR}` as a placeholder for the repository root. Before running tests locally, replace it with the actual path:
+
+```bash
+cd nextflow/vcf_prepper
+
+REPO_ROOT=$(git rev-parse --show-toplevel) # Get the repository root path; set it manually if you need to
+
+sed -i '' "s|\${BASE_DIR}|${REPO_ROOT}|g" \
+  tests/testdata/input_config.json \
+  subworkflows/local/run_vep/tests/testdata/test_vep_config.ini
+```
+
+> **Note:** On Linux, use `sed -i` instead of `sed -i ''`.
+
+#### 2. Set environment variables
+
+The following environment variables are required by various test modules:
+
+```bash
+export ENSEMBL_ROOT_DIR=${REPO_ROOT}/nextflow/vcf_prepper/repos
+export FTP_NFS_DIR=${REPO_ROOT}/nextflow/vcf_prepper/tests/testdata
+export OLD_FTP_NFS_DIR=${REPO_ROOT}/nextflow/vcf_prepper/tests/testdata
+export PLUGIN_DATA_DIR=${REPO_ROOT}/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata
 ```
 
-Note: generated by `with-dag` param of nextflow.
\ No newline at end of file
+Make sure the `repos` directory contains the required Ensembl repositories (see [Pre-requisite](#repositories)).
+
+
+#### 2. Set up test databases
+
+Some tests require a local MySQL instance with test databases loaded:
+
+```bash
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;'
+mysql -h 127.0.0.1 -u root ensembl_genome_metadata < src/python/tests/variation_utils/data/ensembl_genome_metadata.dump
+
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;'
+mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump
+```
+
+#### 4. Run nf-test
+
+```bash
+# Run all tests
+nf-test test .
+
+# Run a specific test file
+nf-test test tests/main.nf.test
+
+# Run tests with coverage
+nf-test test . --coverage
+```
+
+### Running pytest for ensembl-variation-utils
+
+The `ensembl-variation-utils` Python package has its own test suite under `src/python/tests/`.
+
+#### 1. Install the package and test dependencies
+
+```bash
+cd <repo_root>
+pip install src/python
+pip install pytest coverage
+```
+
+#### 2. Set up test databases
+
+Some tests require a local MySQL instance with test databases loaded:
+
+```bash
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;'
+mysql -h 127.0.0.1 -u root ensembl_genome_metadata < src/python/tests/variation_utils/data/ensembl_genome_metadata.dump
+
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;'
+mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump
+```
+
+#### 3. Run pytest
+
+```bash
+# Run all tests
+pytest src/python
+
+# Run with coverage
+coverage run -m pytest src/python
+coverage report
+```
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/example_DEFAULT.ini b/nextflow/vcf_prepper/assets/examples/example_DEFAULT.ini
similarity index 100%
rename from nextflow/vcf_prepper/assets/example_DEFAULT.ini
rename to nextflow/vcf_prepper/assets/examples/example_DEFAULT.ini
diff --git a/nextflow/vcf_prepper/assets/example_input_config.json b/nextflow/vcf_prepper/assets/examples/example_input_config.json
similarity index 95%
rename from nextflow/vcf_prepper/assets/example_input_config.json
rename to nextflow/vcf_prepper/assets/examples/example_input_config.json
index c0fe50fd..7e95e36f 100755
--- a/nextflow/vcf_prepper/assets/example_input_config.json
+++ b/nextflow/vcf_prepper/assets/examples/example_input_config.json
@@ -1,7 +1,7 @@
 {
   "homo_sapiens_grch38": [
     {
-      "genome_uuid": "a7335667-93e7-11ec-a39d-005056b38ce3",
+      "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
       "species": "homo_sapiens",
       "assembly": "GRCh38",
       "source_name": "dbSNP",
diff --git a/nextflow/vcf_prepper/assets/examples/example_vep_config.json b/nextflow/vcf_prepper/assets/examples/example_vep_config.json
new file mode 100644
index 00000000..a98a85e4
--- /dev/null
+++ b/nextflow/vcf_prepper/assets/examples/example_vep_config.json
@@ -0,0 +1,49 @@
+{
+  "annotation_source": {
+    "cache": {
+      "active": true
+    },
+    "fasta": {
+      "active": true
+    },
+    "gff": {
+      "active": false
+    }
+  },
+  "default_options": {
+    "force_overwrite": 1,
+    "fork": 2,
+    "vcf": 1,
+    "spdi": 1,
+    "variant_class": 1,
+    "protein": 1,
+    "transcript_version": 1,
+    "gencode_promoter": 1,
+    "offline": 1
+  },
+  "plugins": {
+    "factory": "ABCDEFGHIJKLMNOP",
+    "confs": [
+      {
+        "name": "CADD",
+        "requires_file": true,
+        "keyed": true
+      },
+      {
+        "name": "Phenotypes",
+        "requires_file": true,
+        "keyed": true,
+        "params": [
+            {"id_match": 1}
+        ]
+      }
+    ]
+  },
+  "custom_annotaions": {
+    "confs": [
+      {
+        "name": "frequency"
+      }
+    ]
+  }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/data/test_removevariants.vcf.gz b/nextflow/vcf_prepper/assets/examples/test.vcf.gz
similarity index 100%
rename from nextflow/vcf_prepper/tests/data/test_removevariants.vcf.gz
rename to nextflow/vcf_prepper/assets/examples/test.vcf.gz
diff --git a/nextflow/vcf_prepper/tests/data/test_removevariants.vcf.gz.tbi b/nextflow/vcf_prepper/assets/examples/test.vcf.gz.tbi
similarity index 100%
rename from nextflow/vcf_prepper/tests/data/test_removevariants.vcf.gz.tbi
rename to nextflow/vcf_prepper/assets/examples/test.vcf.gz.tbi
diff --git a/nextflow/vcf_prepper/assets/population_data.json b/nextflow/vcf_prepper/assets/population_data.json
index 21ab3022..e0d578c1 100644
--- a/nextflow/vcf_prepper/assets/population_data.json
+++ b/nextflow/vcf_prepper/assets/population_data.json
@@ -395,7 +395,205 @@
          ]
       }
    ],
-   "homo_sapiens_gca\\d{9}v\\d{1}": [
+   "homo_sapiens_gca009914755v4": [
+      {
+         "name": "gnomAD_exomes",
+         "version": "4.1",
+         "files": [
+            {
+               "version": "4.1",
+               "short_name": "gnomAD_exomes",
+               "file_location": "/nfs/production/flicek/ensembl/production/ensemblftp/rapid-release/species/Homo_sapiens/##ASSEMBLY_ACC##/ensembl/variation/2022_10/vcf/2024_07/gnomad.exomes.v4.1.sites.##ASSEMBLY_ACC##.trimmed_liftover.vcf.gz",
+               "include_fields": [
+                  {
+                     "name": "gnomADe:ALL",
+                     "fields": {
+                        "af": "AF",
+                        "ac": "AC",
+                        "an": "AN"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:afr",
+                     "fields": {
+                        "af": "AF_afr",
+                        "ac": "AC_afr",
+                        "an": "AN_afr"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:amr",
+                     "fields": {
+                        "af": "AF_amr",
+                        "ac": "AC_amr",
+                        "an": "AN_amr"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:asj",
+                     "fields": {
+                        "af": "AF_asj",
+                        "ac": "AC_asj",
+                        "an": "AN_asj"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:eas",
+                     "fields": {
+                        "af": "AF_eas",
+                        "ac": "AC_eas",
+                        "an": "AN_eas"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:fin",
+                     "fields": {
+                        "af": "AF_fin",
+                        "ac": "AC_fin",
+                        "an": "AN_fin"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:mid",
+                     "fields": {
+                        "af": "AF_mid",
+                        "ac": "AC_mid",
+                        "an": "AN_mid"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:nfe",
+                     "fields": {
+                        "af": "AF_nfe",
+                        "ac": "AC_nfe",
+                        "an": "AN_nfe"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:remaining",
+                     "fields": {
+                        "af": "AF_remaining",
+                        "ac": "AC_remaining",
+                        "an": "AN_remaining"
+                     }
+                  },
+                  {
+                     "name": "gnomADe:sas",
+                     "fields": {
+                        "af": "AF_sas",
+                        "ac": "AC_sas",
+                        "an": "AN_sas"
+                     }
+                  }
+               ]
+            }
+         ]
+      },
+      {
+         "name": "gnomAD_genomes",
+         "version": "4.1",
+         "representative": true,
+         "files": [
+            {
+               "version": "4.1",
+               "short_name": "gnomAD_genomes",
+               "representative_af_field": "AF",
+               "file_location": "/nfs/production/flicek/ensembl/production/ensemblftp/rapid-release/species/Homo_sapiens/##ASSEMBLY_ACC##/ensembl/variation/2022_10/vcf/2024_07/gnomad.genomes.v4.1.sites.##ASSEMBLY_ACC##.trimmed_liftover.vcf.gz",
+               "include_fields": [
+                  {
+                     "name": "gnomADg:ALL",
+                     "fields": {
+                        "af": "AF",
+                        "ac": "AC",
+                        "an": "AN"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:afr",
+                     "fields": {
+                        "af": "AF_afr",
+                        "ac": "AC_afr",
+                        "an": "AN_afr"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:ami",
+                     "fields": {
+                        "af": "AF_ami",
+                        "ac": "AC_ami",
+                        "an": "AN_ami"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:amr",
+                     "fields": {
+                        "af": "AF_amr",
+                        "ac": "AC_amr",
+                        "an": "AN_amr"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:asj",
+                     "fields": {
+                        "af": "AF_asj",
+                        "ac": "AC_asj",
+                        "an": "AN_asj"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:eas",
+                     "fields": {
+                        "af": "AF_eas",
+                        "ac": "AC_eas",
+                        "an": "AN_eas"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:fin",
+                     "fields": {
+                        "af": "AF_fin",
+                        "ac": "AC_fin",
+                        "an": "AN_fin"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:mid",
+                     "fields": {
+                        "af": "AF_mid",
+                        "ac": "AC_mid",
+                        "an": "AN_mid"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:nfe",
+                     "fields": {
+                        "af": "AF_nfe",
+                        "ac": "AC_nfe",
+                        "an": "AN_nfe"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:remaining",
+                     "fields": {
+                        "af": "AF_remaining",
+                        "ac": "AC_remaining",
+                        "an": "AN_remaining"
+                     }
+                  },
+                  {
+                     "name": "gnomADg:sas",
+                     "fields": {
+                        "af": "AF_sas",
+                        "ac": "AC_sas",
+                        "an": "AN_sas"
+                     }
+                  }
+               ]
+            }
+         ]
+      }
+   ],
+   "homo_sapiens_gca018[458][05-7][0-79]\\d{2}5v1": [
       {
          "name": "gnomAD_exomes",
          "version": "4.1",
@@ -1071,6 +1269,25 @@
       }
    ],
    "triticum_aestivum": [
+      {
+         "name": "MAGIC-16-Diversity",
+         "files": [
+            {
+               "file_location": "/nfs/production/flicek/ensembl/variation/new_website/vep/custom_data/frequency_projects/triticum_aestivum/IWGSC/MAGIC.vcf.gz",
+               "short_name": "MAGIC-16-Diversity",
+               "include_fields": [
+                  {
+                     "name": "MAGIC-16-Diversity",
+                     "fields": {
+                        "af": "AF",
+                        "ac": "AC",
+                        "an": "AN"
+                     }
+                  }
+               ]
+            }
+         ]
+      },
       {
          "name": "Axiom",
          "files": [
diff --git a/nextflow/vcf_prepper/assets/schema/input_config.json b/nextflow/vcf_prepper/assets/schema/input_config.json
new file mode 100644
index 00000000..8ff5a33d
--- /dev/null
+++ b/nextflow/vcf_prepper/assets/schema/input_config.json
@@ -0,0 +1,79 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type": "object",
+    "properties": {
+        "genome_uuid": {
+            "type": "object",
+            "description": "genome_uuid of the genome",
+            "properties": {
+                "species": {
+                    "type": "string"
+                },
+                "assembly": {
+                    "type": "string"
+                },
+                "files": {
+                    "type": "array",
+                    "items": [
+                        {
+                            "type": "object",
+                            "properties": {
+                                "file_type": {
+                                    "type": "string"
+                                },
+                                "file_location": {
+                                    "type": "string"
+                                },
+                                "sources": {
+                                    "type": "array",
+                                    "items": [
+                                        {
+                                            "type": "object",
+                                            "properties": {
+                                                "name": {
+                                                    "type": "string"
+                                                },
+                                                "version": {
+                                                    "type": "string"
+                                                },
+                                                "description": {
+                                                    "type": "string"
+                                                },
+                                                "url": {
+                                                    "type": "string"
+                                                },
+                                                "accession_url": {
+                                                    "type": "string"
+                                                }
+                                            },
+                                            "required": [
+                                                "name",
+                                                "version",
+                                                "description",
+                                                "url",
+                                                "accession_url"
+                                            ]
+                                        }
+                                    ]
+                                }
+                            },
+                            "required": [
+                                "file_type",
+                                "file_location",
+                                "sources"
+                            ]
+                        }
+                    ]
+                }
+            },
+            "required": [
+                "species",
+                "assembly",
+                "files"
+            ]
+        }
+    },
+    "required": [
+        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb"
+    ]
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/schema/vep_config.json b/nextflow/vcf_prepper/assets/schema/vep_config.json
new file mode 100644
index 00000000..9d71325b
--- /dev/null
+++ b/nextflow/vcf_prepper/assets/schema/vep_config.json
@@ -0,0 +1,267 @@
+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "type": "object",
+  "properties": {
+    "annotation_source": {
+      "type": "object",
+      "properties": {
+        "cache": {
+          "type": "object",
+          "properties": {
+            "active": {
+              "type": "boolean"
+            },
+            "dir": {
+              "type": "string"
+            },
+            "version": {
+              "type": "integer"
+            },
+            "factory": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "active",
+            "dir",
+            "version",
+            "factory"
+          ]
+        },
+        "fasta": {
+          "type": "object",
+          "properties": {
+            "active": {
+              "type": "boolean"
+            },
+            "dir": {
+              "type": "string"
+            },
+            "file": {
+              "type": "string"
+            },
+            "factory": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "active",
+            "dir",
+            "file",
+            "factory"
+          ]
+        },
+        "gff": {
+          "type": "object",
+          "properties": {
+            "active": {
+              "type": "boolean"
+            },
+            "dir": {
+              "type": "string"
+            },
+            "file": {
+              "type": "string"
+            },
+            "factory": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "active",
+            "dir",
+            "file",
+            "factory"
+          ]
+        }
+      },
+      "required": [
+        "cache",
+        "fasta",
+        "gff"
+      ]
+    },
+    "default_options": {
+      "type": "object",
+      "properties": {
+        "force_overwrite": {
+          "type": "integer"
+        },
+        "fork": {
+          "type": "integer"
+        },
+        "buffer_size": {
+          "type": "integer"
+        },
+        "vcf": {
+          "type": "integer"
+        },
+        "spdi": {
+          "type": "integer"
+        },
+        "variant_class": {
+          "type": "integer"
+        },
+        "protein": {
+          "type": "integer"
+        },
+        "transcript_version": {
+          "type": "integer"
+        },
+        "gencode_promoter": {
+          "type": "integer"
+        },
+        "offline": {
+          "type": "integer"
+        },
+        "sift": {
+          "type": "integer"
+        },
+        "polyphen": {
+          "type": "integer"
+        },
+        "af_1kg": {
+          "type": "integer"
+        }
+      },
+      "required": [
+        "force_overwrite",
+        "fork",
+        "buffer_size",
+        "vcf",
+        "spdi",
+        "variant_class",
+        "protein",
+        "transcript_version",
+        "gencode_promoter",
+        "offline",
+        "sift",
+        "polyphen"
+      ]
+    },
+    "plugins": {
+      "type": "object",
+      "properties": {
+        "genome_matcher": {
+          "type": "string"
+        },
+        "confs": {
+          "type": "array",
+          "items": [
+            {
+              "type": "object",
+              "properties": {
+                "name": {
+                  "type": "string"
+                },
+                "requires_file": {
+                  "type": "boolean"
+                },
+                "keyed": {
+                  "type": "boolean"
+                },
+                "args": {
+                  "type": "array",
+                  "items": [
+                    {
+                      "type": "object",
+                      "properties": {
+                        "key": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "key"
+                      ]
+                    }
+                  ]
+                }
+              },
+              "required": [
+                "name",
+                "requires_file",
+                "keyed",
+                "args"
+              ]
+            }
+          ]
+        }
+      },
+      "required": [
+        "genome_matcher",
+        "confs"
+      ]
+    },
+    "custom_annotaions": {
+      "type": "object",
+      "properties": {
+        "genome_matcher": {
+          "type": "string"
+        },
+        "confs": {
+          "type": "array",
+          "items": [
+            {
+              "type": "object",
+              "properties": {
+                "name": {
+                  "type": "string"
+                },
+                "genome_matcher": {
+                  "type": "string"
+                },
+                "args": {
+                  "type": "array",
+                  "items": [
+                    {
+                      "type": "object",
+                      "properties": {
+                        "short_name": {
+                          "type": "string"
+                        },
+                        "file": {
+                          "type": "string"
+                        },
+                        "format": {
+                          "type": "string"
+                        },
+                        "type": {
+                          "type": "string"
+                        },
+                        "coord": {
+                          "type": "integer"
+                        }
+                      },
+                      "required": [
+                        "short_name",
+                        "file",
+                        "format",
+                        "type",
+                        "coord"
+                      ]
+                    }
+                  ]
+                }
+              },
+              "required": [
+                "name",
+                "genome_matcher",
+                "args"
+              ]
+            }
+          ]
+        }
+      },
+      "required": [
+        "genome_matcher",
+        "confs"
+      ]
+    }
+  },
+  "required": [
+    "annotation_source",
+    "default_options",
+    "plugins",
+    "custom_annotaions"
+  ]
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/short_variant_bedfields.json b/nextflow/vcf_prepper/assets/short_variant_bedfields.json
new file mode 100644
index 00000000..afb65078
--- /dev/null
+++ b/nextflow/vcf_prepper/assets/short_variant_bedfields.json
@@ -0,0 +1,42 @@
+{
+	"name": "short_variant",
+	"description": "BED fields for short variant track in genome browser",
+	"fields": {
+		"chromosome": {
+			"type": "string",
+			"pos": 1
+		},
+		"start": {
+			"type": "uint",
+			"pos": 2
+		},
+		"end": {
+			"type": "uint",
+			"pos": 3
+		},
+		"id": {
+			"type": "string",
+			"pos": 4
+		},
+		"variety": {
+			"type": "lstring",
+			"pos": 5
+		},
+		"reference": {
+			"type": "lstring",
+			"pos": 6
+		},
+		"alts": {
+			"type": "lstring",
+			"pos": 7
+		},
+		"group": {
+			"type": "ubyte",
+			"pos": 8
+		},
+		"severity": {
+			"type": "lstring",
+			"pos": 9
+		}
+	}	
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/sources_meta.json b/nextflow/vcf_prepper/assets/sources_meta.json
index 1c173ffe..fd872b0e 100755
--- a/nextflow/vcf_prepper/assets/sources_meta.json
+++ b/nextflow/vcf_prepper/assets/sources_meta.json
@@ -1,149 +1,180 @@
 [
-  {
-    "name": "Ensembl",
-    "version": "110",
-    "description": "Ensembl",
-    "url": "https://beta.ensembl.org",
-    "accession_url": "https://beta.ensembl.org/"
-  },
-  {
-    "name": "dbSNP",
-    "version": "157",
-    "description": "NCBI db of human variants",
-    "url": "https://www.ncbi.nlm.nih.gov/snp/",
-    "accession_url": "https://www.ncbi.nlm.nih.gov/snp/"
-  },
-  {
-    "name": "EVA",
-    "version": "7",
-    "description": "European Variation Archive",
-    "url": "https://www.ebi.ac.uk/eva",
-    "accession_url": "https://www.ebi.ac.uk/eva/?variant&accessionID="
-  },
-  {
-    "name": "The_1001_Genomes_Project",
-    "version": "2016",
-    "description": "The 1001 Genomes Project provides a catalog of genetic variation in the reference plant Arabidopsis thaliana. Launched at the beginning of 2008 to discover sequence variation in at least 1001 strains (accessions). Since 2010, several sets of genomes have been released. The first phase of the project was completed in 2016 with publication of a detailed analysis of 1,135 genomes.",
-    "url": "http://1001genomes.org/"
-  },
-  {
-    "name": "Nordborg",
-    "description": "Variation annotations from Nordborg"
-  },
-  {
-    "name": "IBSC",
-    "version": "0",
-    "description": "International Barley Sequencing Consortium, remapped to MorexV3_pseudomolecules_assembly",
-    "url": "http://europepmc.org/abstract/MED/23075845"
-  },
-  {
-    "name": "Ensembl_Plants",
-    "version": "0",
-    "description": "Previous release of Ensembl Plants"
-  },
-  {
-    "name": "iSelect",
-    "version": "0",
-    "description": "Illumina iSelect SNP chip IDs",
-    "url": "http://bioinf.hutton.ac.uk/iselect/app/"
-  },
-  {
-    "name": "JHI",
-    "version": "0",
-    "description": "James Hutton Institute, Dundee, United Kingdom",
-    "url": "https://ics.hutton.ac.uk/50k/"
-  },
-  {
-    "name": "Gramene_QTLdb",
-    "version": "1",
-    "description": "QTLs from the legacy Gramene QTL Database",
-    "url": "http://archive.gramene.org/db/qtl/"
-  },
-  {
-    "name": "gramene-marker",
-    "version": "1",
-    "description": "gramene markers",
-    "url": "http://archive.gramene.org/markers"
-  },
-  {
-    "name": "Qtaro_QTLdb",
-    "version": "1",
-    "description": "QTLs from the Qtaro Database and remapped to IRGSPv1 assembly by keygen",
-    "url": "http://qtaro.abr.affrc.go.jp/qtab/table"
-  },
-  {
-    "name": "The_150_TGRSP",
-    "version": "1",
-    "description": "The 150 Tomato Genome ReSequencing Project (150 TGRSP) is revealing the genetic variation available in tomato, one of the most important vegetable crops, for breeding in the face of climate change, sustainability, and demand for more and better food",
-    "url": "http://www.tomatogenome.net/"
-  },
-  {
-    "name": "Addo-Quayes_study",
-    "description": "Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of EMS Mutagenized Sorghum"
-  },
-  {
-    "name": "Yinping-Jiao-2016-Study",
-    "description": "(Recalls projected against sorghum bicolor v3.1) EMS induced mutations in Sorghum as an Efficient Platform for Gene Discovery in Grasses"
-  },
-  {
-    "name": "Lozano_study",
-    "description": "Whole genome resequencing of 499 sorghum lines from three sources - Mace (42), TERRA-MEPP (254), and TERRA-REF (203) to study deleterious mutations in sorghum."
-  },
-  {
-    "name": "Sorghum_QTL_Atlas",
-    "version": "1",
-    "description": "QTLs from the the Sorghum QTL Atlas Database developed by Emma Mace group",
-    "url": "https://aussorgm.org.au/sorghum-qtl-atlas/"
-  },
-  {
-    "name": "Lozano_study",
-    "version": "1",
-    "description": "QTLs from the Qtaro Database and remapped to IRGSPv1 assembly by keygen",
-    "url": "http://qtaro.abr.affrc.go.jp/qtab/table"
-  },
-  {
-    "name": "CerealsDB",
-    "description": "Markers from Axiom 820K and 35K SNP Array  provided by <a href='http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php'>CerealsDB<a/>n"
-  },
-  {
-    "name": "EMS-induced mutation",
-    "description": "<a href='http://plants.ensembl.org/Triticum_aestivum/Info/Annotation/#variation'>EMS-induced mutations</a> from sequenced wheat TILLING populations. Seeds can be ordered from <a href='https://www.seedstor.ac.uk/shopping-cart-tilling.php'>UK SeedStor</a> or <a href='http://dubcovskylab.ucdavis.edu/wheat-tilling'>US Dubcovsky lab</a>. Line identifier is variant name up to dot (e.g Kronos3128)."
-  },
-  {
-    "name": "Inter-homoeologous",
-    "description": "Inter-Homoeologous Variants (IHVs) called by alignments of the A,B and D component genomes"
-  },
-  {
-    "name": "Nottingham_WRC",
-    "description": "Markers from Axiom Wheat Relatives Array provided by <a href='https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/axiom_download.php'>CerealsDB</a> and from <a href='https://europepmc.org/article/MED/31465620'> Grewal et al., 2020</a>"
-  },
-  {
-    "name": "Watkins-exome-capture",
-    "description": "103 accessions of the Watkins landrace collection"
-  },
-  {
-    "name": "Exome_Capture_Diversity",
-    "description": "890 diverse wheat landraces and cultivars from <a href='http://wheatgenomics.plantpath.ksu.edu/1000EC/'>He et al</a>"
-  },
-  {
-    "name": "Watkins_collection",
-    "description": "Variants from the the Watkins Collection which is a diverse assortment of heritage wheat varieties from the 1930s, preserved for its unique genetic potential in modern breeding"
-  },
-  {
-    "name": "CNR-ITB",
-    "description": "Markers from Axiom 820K, 35K and iSelect 90K SNP Infinium are provided by <a href='http://www.cerealsdb.uk.net'>CerealsDB</a>. Markers from TaBW280K Affymetrix arrary refer to <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749704/#!po=58.6957'>Rimbert, H. et al.</a>"
-  },
-  {
-    "name": "CSHL/Cornell",
-    "version": "1",
-    "description": "Cold Spring Harbor Laboratory / Cornell University [remapped to PN40024.v4]"
-  },
-  {
-    "name": "HapMap2",
-    "description": "Remapped to Zm-B73-REFERENCE-NAM-5.0"
-  },
-  {
-    "name": "Panzea_2.7GBS",
-    "description": "Remapped to Zm-B73-REFERENCE-NAM-5.0"
-  }
+    {
+        "name": "Ensembl",
+        "version": "110",
+        "description": "Ensembl",
+        "url": "https://beta.ensembl.org",
+        "accession_url": "https://beta.ensembl.org/"
+    },
+    {
+        "name": "dbSNP",
+        "version": "157",
+        "description": "NCBI db of human variants",
+        "url": "https://www.ncbi.nlm.nih.gov/snp/",
+        "accession_url": "https://www.ncbi.nlm.nih.gov/snp/"
+    },
+    {
+        "name": "EVA",
+        "version": "8",
+        "description": "European Variation Archive",
+        "url": "https://www.ebi.ac.uk/eva",
+        "accession_url": "https://www.ebi.ac.uk/eva/?variant&accessionID="
+    },
+    {
+        "name": "The_1001_Genomes_Project",
+        "version": "2016",
+        "description": "The 1001 Genomes Project provides a catalog of genetic variation in the reference plant Arabidopsis thaliana. Launched at the beginning of 2008 to discover sequence variation in at least 1001 strains (accessions). Since 2010, several sets of genomes have been released. The first phase of the project was completed in 2016 with publication of a detailed analysis of 1,135 genomes.",
+        "url": "http://1001genomes.org/"
+    },
+    {
+        "name": "Nordborg",
+        "description": "Variation annotations from Nordborg"
+    },
+    {
+        "name": "IBSC",
+        "version": "0",
+        "description": "International Barley Sequencing Consortium, remapped to MorexV3_pseudomolecules_assembly",
+        "url": "http://europepmc.org/abstract/MED/23075845"
+    },
+    {
+        "name": "Ensembl_Plants",
+        "version": "0",
+        "description": "Previous release of Ensembl Plants"
+    },
+    {
+        "name": "iSelect",
+        "version": "0",
+        "description": "Illumina iSelect SNP chip IDs",
+        "url": "http://bioinf.hutton.ac.uk/iselect/app/"
+    },
+    {
+        "name": "JHI",
+        "version": "0",
+        "description": "James Hutton Institute, Dundee, United Kingdom",
+        "url": "https://ics.hutton.ac.uk/50k/"
+    },
+    {
+        "name": "Gramene_QTLdb",
+        "version": "1",
+        "description": "QTLs from the legacy Gramene QTL Database",
+        "url": "http://archive.gramene.org/db/qtl/"
+    },
+    {
+        "name": "gramene-marker",
+        "version": "1",
+        "description": "gramene markers",
+        "url": "http://archive.gramene.org/markers"
+    },
+    {
+        "name": "Qtaro_QTLdb",
+        "version": "1",
+        "description": "QTLs from the Qtaro Database and remapped to IRGSPv1 assembly by keygen",
+        "url": "http://qtaro.abr.affrc.go.jp/qtab/table"
+    },
+    {
+        "name": "The_150_TGRSP",
+        "version": "1",
+        "description": "The 150 Tomato Genome ReSequencing Project (150 TGRSP) is revealing the genetic variation available in tomato, one of the most important vegetable crops, for breeding in the face of climate change, sustainability, and demand for more and better food",
+        "url": "http://www.tomatogenome.net/"
+    },
+    {
+        "name": "Addo-Quayes_study",
+        "description": "Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of EMS Mutagenized Sorghum"
+    },
+    {
+        "name": "Yinping-Jiao-2016-Study",
+        "description": "(Recalls projected against sorghum bicolor v3.1) EMS induced mutations in Sorghum as an Efficient Platform for Gene Discovery in Grasses"
+    },
+    {
+        "name": "Lozano_study",
+        "description": "Whole genome resequencing of 499 sorghum lines from three sources - Mace (42), TERRA-MEPP (254), and TERRA-REF (203) to study deleterious mutations in sorghum."
+    },
+    {
+        "name": "Sorghum_QTL_Atlas",
+        "version": "1",
+        "description": "QTLs from the the Sorghum QTL Atlas Database developed by Emma Mace group",
+        "url": "https://aussorgm.org.au/sorghum-qtl-atlas/"
+    },
+    {
+        "name": "Lozano_study",
+        "version": "1",
+        "description": "QTLs from the Qtaro Database and remapped to IRGSPv1 assembly by keygen",
+        "url": "http://qtaro.abr.affrc.go.jp/qtab/table"
+    },
+    {
+        "name": "CerealsDB",
+        "description": "Markers from Axiom 820K and 35K SNP Array  provided by <a href='http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php'>CerealsDB<a/>n"
+    },
+    {
+        "name": "EMS-induced mutation",
+        "description": "<a href='http://plants.ensembl.org/Triticum_aestivum/Info/Annotation/#variation'>EMS-induced mutations</a> from sequenced wheat TILLING populations. Seeds can be ordered from <a href='https://www.seedstor.ac.uk/shopping-cart-tilling.php'>UK SeedStor</a> or <a href='http://dubcovskylab.ucdavis.edu/wheat-tilling'>US Dubcovsky lab</a>. Line identifier is variant name up to dot (e.g Kronos3128)."
+    },
+    {
+        "name": "Inter-homoeologous",
+        "description": "Inter-Homoeologous Variants (IHVs) called by alignments of the A,B and D component genomes"
+    },
+    {
+        "name": "Nottingham_WRC",
+        "description": "Markers from Axiom Wheat Relatives Array provided by <a href='https://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/axiom_download.php'>CerealsDB</a> and from <a href='https://europepmc.org/article/MED/31465620'> Grewal et al., 2020</a>"
+    },
+    {
+        "name": "Watkins-exome-capture",
+        "description": "103 accessions of the Watkins landrace collection"
+    },
+    {
+        "name": "Exome_Capture_Diversity",
+        "description": "890 diverse wheat landraces and cultivars from <a href='http://wheatgenomics.plantpath.ksu.edu/1000EC/'>He et al</a>"
+    },
+    {
+        "name": "Watkins_collection",
+        "description": "Variants from the the Watkins Collection which is a diverse assortment of heritage wheat varieties from the 1930s, preserved for its unique genetic potential in modern breeding"
+    },
+    {
+        "name": "ENA",
+        "description": "Variants from the European Nucleotide Archive (ENA)"
+    },
+    {
+        "name": "CNR-ITB",
+        "description": "Markers from Axiom 820K, 35K and iSelect 90K SNP Infinium are provided by <a href='http://www.cerealsdb.uk.net'>CerealsDB</a>. Markers from TaBW280K Affymetrix arrary refer to <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749704/#!po=58.6957'>Rimbert, H. et al.</a>"
+    },
+    {
+        "name": "CSHL/Cornell",
+        "version": "1",
+        "description": "Cold Spring Harbor Laboratory / Cornell University [remapped to PN40024.v4]"
+    },
+    {
+        "name": "HapMap2",
+        "description": "Remapped to Zm-B73-REFERENCE-NAM-5.0"
+    },
+    {
+        "name": "Panzea_2.7GBS",
+        "description": "Remapped to Zm-B73-REFERENCE-NAM-5.0"
+    },
+    {
+        "name": "ClinVar",
+        "version": "2025-11-09",
+        "description": "ClinVar is a free public archive of reports of the relationships between human variations and phenotypes.",
+        "url": "https://www.ncbi.nlm.nih.gov/clinvar/",
+        "accession_url": "https://www.ncbi.nlm.nih.gov/clinvar/variation/"
+    },
+    {
+        "name": "HGSVC3",
+        "version": "2025-03-01",
+        "description": "The Human Genome Structural Variation Consortium (HGSVC, Phase 3) focus on developing resources and computational approaches to fully characterize and integrate structural variants into their haplotypic context in order to understand their mutational mechanisms and functional consequences",
+        "url": "https://www.hgsvc.org/about"
+    },
+    {
+        "name": "nstd166",
+        "version": "2021-08-30",
+        "description": "(dbVar study) The v2.1 release of gnomAD-SV represents a catalogue of structural variants (SVs) discovered from whole-genome sequencing of 14,891 individuals at 32X mean coverage with 2x150bp Illumina reads. From this dataset, site-level SV data was able to be released for 10,847 unrelated individuals with appropriate consent for broad data sharing",
+        "url": "https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd166",
+        "accession_url": "https://www.ncbi.nlm.nih.gov/dbvar/variants/"
+    },
+    {
+        "name": "nstd102",
+        "version": "2026-01-13",
+        "description": "(dbVar Study) Structural Variants with clinical assertions, submitted to ClinVar by external labs. dbVar now imports all placements from ClinVar as \"submitted\" and only remaps what is missing in order to place all variants on both GRCh37 and GRCh38.",
+        "url": "https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd102",
+        "accession_url": "https://www.ncbi.nlm.nih.gov/dbvar/variants/"
+    }
 ]
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/structural_variant_bedfields.json b/nextflow/vcf_prepper/assets/structural_variant_bedfields.json
new file mode 100644
index 00000000..d8a8b17e
--- /dev/null
+++ b/nextflow/vcf_prepper/assets/structural_variant_bedfields.json
@@ -0,0 +1,46 @@
+{
+    "name": "structural_variant",
+    "description": "BED fields for structural variant track in genome browser",
+    "fields": {
+        "chromosome": {
+            "type": "string",
+            "pos": 1
+        },
+        "start": {
+            "type": "uint",
+            "pos": 2
+        },
+        "end": {
+            "type": "uint",
+            "pos": 3
+        },
+        "id": {
+            "type": "string",
+            "pos": 4
+        },
+        "variety": {
+            "type": "lstring",
+            "pos": 5
+        },
+        "reference": {
+            "type": "lstring",
+            "pos": 6
+        },
+        "alts": {
+            "type": "lstring",
+            "pos": 7
+        },
+        "group": {
+            "type": "ubyte",
+            "pos": 8
+        },
+        "severity": {
+            "type": "lstring",
+            "pos": 9
+        },
+        "extent": {
+            "type": "int",
+            "pos": 10
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/assets/variation_consequnce_rank.json b/nextflow/vcf_prepper/assets/variation_consequnce_rank.json
index dc166f49..2924d1b1 100644
--- a/nextflow/vcf_prepper/assets/variation_consequnce_rank.json
+++ b/nextflow/vcf_prepper/assets/variation_consequnce_rank.json
@@ -1,43 +1,43 @@
 {
-   "feature_truncation" : "10",
-   "incomplete_terminal_codon_variant" : "19",
-   "inframe_insertion" : "11",
-   "regulatory_region_variant" : "39",
-   "3_prime_UTR_variant" : "26",
-   "stop_gained" : "4",
-   "stop_retained_variant" : "21",
-   "regulatory_region_amplification" : "38",
-   "transcript_amplification" : "8",
-   "protein_altering_variant" : "14",
-   "transcript_ablation" : "1",
+   "frameshift_variant" : "5",
+   "regulatory_region_ablation" : "37",
+   "sequence_variant" : "41",
+   "splice_donor_variant" : "3",
+   "splice_polypyrimidine_tract_variant" : "18",
    "splice_acceptor_variant" : "2",
-   "missense_variant" : "13",
-   "coding_sequence_variant" : "23",
+   "splice_donor_region_variant" : "17",
    "inframe_deletion" : "12",
-   "feature_elongation" : "9",
-   "TF_binding_site_variant" : "36",
+   "synonymous_variant" : "22",
+   "incomplete_terminal_codon_variant" : "19",
+   "coding_sequence_variant" : "23",
+   "upstream_gene_variant" : "32",
+   "coding_transcript_variant" : "31",
    "5_prime_UTR_variant" : "25",
-   "sequence_variant" : "41",
+   "downstream_gene_variant" : "33",
+   "feature_elongation" : "9",
    "mature_miRNA_variant" : "24",
-   "NMD_transcript_variant" : "29",
-   "synonymous_variant" : "22",
-   "regulatory_region_ablation" : "37",
+   "start_lost" : "7",
+   "intergenic_variant" : "40",
+   "transcript_ablation" : "1",
+   "intron_variant" : "28",
+   "start_retained_variant" : "20",
+   "non_coding_transcript_exon_variant" : "27",
+   "protein_altering_variant" : "14",
+   "regulatory_region_amplification" : "38",
+   "stop_retained_variant" : "21",
+   "transcript_amplification" : "8",
    "splice_donor_5th_base_variant" : "15",
+   "feature_truncation" : "10",
+   "inframe_insertion" : "11",
    "splice_region_variant" : "16",
+   "3_prime_UTR_variant" : "26",
+   "stop_gained" : "4",
+   "missense_variant" : "13",
    "non_coding_transcript_variant" : "30",
-   "splice_donor_region_variant" : "17",
-   "intergenic_variant" : "40",
-   "TFBS_ablation" : "34",
-   "start_lost" : "7",
    "stop_lost" : "6",
-   "splice_donor_variant" : "3",
+   "NMD_transcript_variant" : "29",
    "TFBS_amplification" : "35",
-   "downstream_gene_variant" : "33",
-   "non_coding_transcript_exon_variant" : "27",
-   "upstream_gene_variant" : "32",
-   "frameshift_variant" : "5",
-   "start_retained_variant" : "20",
-   "coding_transcript_variant" : "31",
-   "intron_variant" : "28",
-   "splice_polypyrimidine_tract_variant" : "18"
+   "TFBS_ablation" : "34",
+   "regulatory_region_variant" : "39",
+   "TF_binding_site_variant" : "36"
 }
diff --git a/nextflow/vcf_prepper/bin/bed_to_wig b/nextflow/vcf_prepper/bin/bed_to_wig
index 142dd977..6b2c72b7 100755
Binary files a/nextflow/vcf_prepper/bin/bed_to_wig and b/nextflow/vcf_prepper/bin/bed_to_wig differ
diff --git a/nextflow/vcf_prepper/bin/generate_chrom_sizes.py b/nextflow/vcf_prepper/bin/generate_chrom_sizes.py
index f52c4d2b..28c549c3 100755
--- a/nextflow/vcf_prepper/bin/generate_chrom_sizes.py
+++ b/nextflow/vcf_prepper/bin/generate_chrom_sizes.py
@@ -15,12 +15,10 @@
 # limitations under the License.
 
 import sys
-import configparser
 import argparse
-import subprocess
 import os
 
-from helper import parse_ini, get_db_name
+from ensembl.variation_utils.clients import core
 
 
 def parse_args(args=None):
@@ -52,109 +50,52 @@ def parse_args(args=None):
         required=False,
         help="file with chromomsome sizes, default - <species>_<assembly>.chrom.sizes in the same directory.",
     )
-    parser.add_argument(
-        "--force",
-        dest="force",
-        action="store_true",
-        help="forcefully create config even if already exists",
-    )
 
     return parser.parse_args(args)
 
 
-def generate_chrom_sizes(
-    server: dict,
-    core_db: str,
-    chrom_sizes: str,
-    assembly: str = "grch38",
-    force: bool = False,
-) -> None:
-    """Generate a chromosome sizes file from the core database.
+def main(args=None):
+    """Main entry point to create chromosome sizes file.
 
-    Writes seq_region lengths and synonym lengths with deduplication.
+    Parses arguments, determines the core DB and invokes generate_chrom_sizes.
 
     Args:
-        server (dict): Server connection mapping.
-        core_db (str): Core database name.
-        chrom_sizes (str): Output chrom sizes filename.
-        assembly (str): Assembly identifier used to filter coord_system.
-        force (bool): If True overwrite existing file.
+        args (list|None): Optional argument list for testing.
 
     Returns:
         None
     """
-    if os.path.exists(chrom_sizes) and not force:
+    args = parse_args(args)
+
+    species = args.species
+    assembly = args.assembly
+    version = args.version
+    chrom_sizes = args.chrom_sizes or f"{species}_{assembly}.chrom.sizes"
+    ini_file = args.ini_file or "DEFAULT.ini"
+    
+    if os.path.exists(chrom_sizes):
         print(f"[INFO] {chrom_sizes} file already exists, skipping ...")
         return
+    
+    core_client = core.CoreDBClient(ini_file=ini_file)
+    core_client.species = species
+    core_client.version = version
 
     query = f"SELECT coord_system_id FROM coord_system WHERE version = '{assembly}';"
-    process = subprocess.run(
-        [
-            "mysql",
-            "--host",
-            server["host"],
-            "--port",
-            server["port"],
-            "--user",
-            server["user"],
-            "--database",
-            core_db,
-            "-N",
-            "--execute",
-            query,
-        ],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
+    query_output = core_client.run_query(query)
     coord_ids = (
-        "(" + ",".join([id for id in process.stdout.decode().strip().split("\n")]) + ")"
+        "(" + ",".join([id for id in query_output.split("\n")]) + ")"
     )
 
     query = f"SELECT name, length FROM seq_region WHERE coord_system_id IN {coord_ids};"
-    process = subprocess.run(
-        [
-            "mysql",
-            "--host",
-            server["host"],
-            "--port",
-            server["port"],
-            "--user",
-            server["user"],
-            "--database",
-            core_db,
-            "-N",
-            "--execute",
-            query,
-        ],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-
+    query_output = core_client.run_query(query)
     with open(chrom_sizes, "w") as file:
-        file.write(process.stdout.decode())
+        file.write(query_output + "\n")
 
     query = f"SELECT ss.synonym, s.length FROM seq_region AS s, seq_region_synonym AS ss WHERE s.seq_region_id = ss.seq_region_id AND s.coord_system_id IN {coord_ids};"
-    process = subprocess.run(
-        [
-            "mysql",
-            "--host",
-            server["host"],
-            "--port",
-            server["port"],
-            "--user",
-            server["user"],
-            "--database",
-            core_db,
-            "-N",
-            "--execute",
-            query,
-        ],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-
+    query_output = core_client.run_query(query)
     with open(chrom_sizes, "a") as file:
-        file.write(process.stdout.decode().strip())
+        file.write(query_output)
 
     # remove duplicates
     with open(chrom_sizes, "r") as file:
@@ -172,29 +113,5 @@ def generate_chrom_sizes(
             length = int(lengths[name]) + 1
             file.write(f"{name}\t{str(length)}\n")
 
-
-def main(args=None):
-    """Main entry point to create chromosome sizes file.
-
-    Parses arguments, determines the core DB and invokes generate_chrom_sizes.
-
-    Args:
-        args (list|None): Optional argument list for testing.
-
-    Returns:
-        None
-    """
-    args = parse_args(args)
-
-    species = args.species
-    assembly = args.assembly
-    chrom_sizes = args.chrom_sizes or f"{species}_{assembly}.chrom.sizes"
-    ini_file = args.ini_file or "DEFAULT.ini"
-    core_server = parse_ini(ini_file, "core")
-    core_db = get_db_name(core_server, args.version, species, type="core")
-
-    generate_chrom_sizes(core_server, core_db, chrom_sizes, assembly, args.force)
-
-
 if __name__ == "__main__":
     sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/generate_synonym_file.py b/nextflow/vcf_prepper/bin/generate_synonym_file.py
index 0db574b9..f166707d 100755
--- a/nextflow/vcf_prepper/bin/generate_synonym_file.py
+++ b/nextflow/vcf_prepper/bin/generate_synonym_file.py
@@ -15,12 +15,11 @@
 # limitations under the License.
 
 import sys
-import configparser
 import argparse
 import subprocess
 import os
 
-from helper import parse_ini, get_db_name
+from ensembl.variation_utils.clients import core
 
 
 def parse_args(args=None):
@@ -52,59 +51,41 @@ def parse_args(args=None):
         required=False,
         help="file with chromomsome synonyms, default - <species>_<assembly>.synonyms in the same directory.",
     )
-    parser.add_argument(
-        "--force",
-        dest="force",
-        action="store_true",
-        help="forcefully create config even if already exists",
-    )
 
     return parser.parse_args(args)
 
 
-def generate_synonym_file(
-    server: dict, core_db: str, synonym_file: str, force: bool = False
-) -> None:
-    """Generate a chromosome synonym file from the core database.
+def main(args=None):
+    """Main entry point to create a synonyms file.
 
-    Queries seq_region and seq_region_synonym tables, post-processes to remove duplicates
-    and resolves names longer than 31 characters where possible.
+    Parses arguments, determines the core database and invokes generate_synonym_file.
 
     Args:
-        server (dict): Server connection mapping.
-        core_db (str): Core database name.
-        synonym_file (str): Output file path.
-        force (bool): If True overwrite existing file, otherwise skip if exists.
+        args (list|None): Optional argument list for testing.
 
     Returns:
         None
     """
-    if os.path.exists(synonym_file) and not force:
+    args = parse_args(args)
+
+    species = args.species
+    assembly = args.assembly
+    version = args.version
+    synonym_file = args.synonym_file or f"{species}_{assembly}.synonyms"
+    ini_file = args.ini_file or "DEFAULT.ini"
+
+    if os.path.exists(synonym_file):
         print(f"[INFO] {synonym_file} file already exists, skipping ...")
         return
+    
+    core_client = core.CoreDBClient(ini_file=ini_file)
+    core_client.species = species
+    core_client.version = version
 
     query = f"SELECT ss.synonym, sr.name FROM seq_region AS sr, seq_region_synonym AS ss WHERE sr.seq_region_id = ss.seq_region_id;"
-    process = subprocess.run(
-        [
-            "mysql",
-            "--host",
-            server["host"],
-            "--port",
-            server["port"],
-            "--user",
-            server["user"],
-            "--database",
-            core_db,
-            "-N",
-            "--execute",
-            query,
-        ],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-
+    query_output = core_client.run_query(query)
     with open(synonym_file, "w") as file:
-        file.write(process.stdout.decode().strip())
+        file.write(query_output)
 
     # remove duplicates and change seq region name that are longer than 31 character
     with open(synonym_file, "r") as file:
@@ -151,28 +132,5 @@ def generate_synonym_file(
             file.write(f"{synonym}\t{new_names[synonym]}\n")
 
 
-def main(args=None):
-    """Main entry point to create a synonyms file.
-
-    Parses arguments, determines the core database and invokes generate_synonym_file.
-
-    Args:
-        args (list|None): Optional argument list for testing.
-
-    Returns:
-        None
-    """
-    args = parse_args(args)
-
-    species = args.species
-    assembly = args.assembly
-    synonym_file = args.synonym_file or f"{species}_{assembly}.synonyms"
-    ini_file = args.ini_file or "DEFAULT.ini"
-    core_server = parse_ini(ini_file, "core")
-    core_db = get_db_name(core_server, args.version, species, type="core")
-
-    generate_synonym_file(core_server, core_db, synonym_file, args.force)
-
-
 if __name__ == "__main__":
     sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/generate_vep_config.py b/nextflow/vcf_prepper/bin/generate_vep_config.py
deleted file mode 100755
index 12bd400b..00000000
--- a/nextflow/vcf_prepper/bin/generate_vep_config.py
+++ /dev/null
@@ -1,662 +0,0 @@
-#!/usr/bin/env python3
-
-# See the NOTICE file distributed with this work for additional information
-# regarding copyright ownership.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import sys
-import configparser
-import argparse
-import subprocess
-import os
-import json
-import re
-import glob
-
-from helper import (
-    parse_ini,
-    get_db_name,
-    get_division,
-    get_fasta_species_name,
-    get_relative_version,
-    Placeholders,
-)
-
-CACHE_DIR = "/nfs/production/flicek/ensembl/variation/data/VEP/tabixconverted"
-FASTA_DIR = "/nfs/production/flicek/ensembl/variation/data/VEP/fasta"
-REPO_DIR = os.path.join("/hps/software/users/ensembl/variation", os.environ.get("USER"))
-PLUGIN_DATA_DIR = "/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/VERSION/vep/plugin_data"
-CONSERVATION_DATA_DIR = "/nfs/production/flicek/ensembl/variation/data/Conservation"
-SIFT_SPECIES = [
-    "homo_sapiens",
-    "homo_sapiens_37",
-    "felis_catus",
-    "gallus_gallus",
-    "bos_taurus",
-    "canis_lupus_familiaris",
-    "capra_hircus",
-    "equus_caballus",
-    "mus_musculus",
-    "sus_scrofa",
-    "rattus_norvegicus",
-    "ovis_aries",
-    "ovis_aries_rambouillet",
-    "danio_rerio",
-]
-POLYPHEN_SPECIES = [
-    "homo_sapiens",
-    "homo_sapiens_37",
-]
-PLUGINS = [
-    "CADD",
-    "REVEL",
-    "SpliceAI",
-    "Phenotypes",
-    "IntAct",
-    "AncestralAllele",
-    "Conservation",
-    "MaveDB",
-    "AlphaMissense",
-    "Downstream",
-    "ClinPred",
-]
-
-
-def parse_args(args=None):
-    """Parse command-line arguments for VEP configuration generation.
-
-    Args:
-        args (list|None): Optional argument list for testing; if None argparse reads sys.argv.
-
-    Returns:
-        argparse.Namespace: Parsed arguments.
-    """
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(dest="version", type=int, help="Ensembl release version")
-    parser.add_argument(dest="species", type=str, help="Species production name")
-    parser.add_argument(dest="assembly", type=str, help="Assembly default")
-    parser.add_argument(
-        "--genome_uuid", dest="genome_uuid", type=str, help="Genome UUID"
-    )
-    parser.add_argument(
-        "--division",
-        dest="division",
-        type=str,
-        required=False,
-        help="Ensembl division the species belongs to",
-    )
-    parser.add_argument(
-        "-I",
-        "--ini_file",
-        dest="ini_file",
-        type=str,
-        required=False,
-        help="full path database configuration file, default - DEFAULT.ini in the same directory.",
-    )
-    parser.add_argument(
-        "--vep_config",
-        dest="vep_config",
-        type=str,
-        required=False,
-        help="VEP configuration file, default - <species>_<assembly>.ini in the same directory.",
-    )
-    parser.add_argument(
-        "--cache_dir",
-        dest="cache_dir",
-        type=str,
-        required=False,
-        help="VEP cache directory, must be indexed",
-    )
-    parser.add_argument(
-        "--fasta_dir",
-        dest="fasta_dir",
-        type=str,
-        required=False,
-        help="Directory containing toplevel FASTA",
-    )
-    parser.add_argument(
-        "--gff_dir",
-        dest="gff_dir",
-        type=str,
-        required=False,
-        help="Directory containing GFF file",
-    )
-    parser.add_argument(
-        "--conservation_data_dir",
-        dest="conservation_data_dir",
-        type=str,
-        required=False,
-        help="Conservation plugin data dir",
-    )
-    parser.add_argument(
-        "--repo_dir",
-        dest="repo_dir",
-        type=str,
-        required=False,
-        help="Ensembl repositories directory",
-    )
-    parser.add_argument(
-        "--population_data_file",
-        dest="population_data_file",
-        type=str,
-        required=False,
-        help="A JSON file containing population information for all species.",
-    )
-    parser.add_argument(
-        "--structural_variant",
-        dest="structural_variant",
-        action="store_true",
-        help="Run for structural variants",
-    )
-    parser.add_argument(
-        "--use_old_infra",
-        dest="use_old_infra",
-        action="store_true",
-        help="Use old infrastructure to get FASTA file",
-    )
-
-    return parser.parse_args(args)
-
-
-def format_custom_args(
-    file: str,
-    short_name: str,
-    format: str = "vcf",
-    type: str = "exact",
-    coords: int = 0,
-    fields: list = [],
-) -> str:
-    """Format a custom annotation argument line for VEP.
-
-    Validates that files matching the file pattern exist (supports placeholder, e.g. - ###CHR###)
-    and returns a single-line 'custom' configuration for the VEP ini.
-
-    Args:
-        file (str): Path or glob pattern for the custom file, may include '###CHR###'.
-        short_name (str): Short name for the custom annotation.
-        format (str): Format of the custom file (default 'vcf').
-        type (str): Matching type (default 'exact').
-        coords (int): Whether coordinates are present (default 0).
-        fields (list): List of field names to include.
-
-    Returns:
-        str: Formatted custom argument line.
-
-    Exits:
-        Exits the script if no file match is found.
-    """
-    check_file_path = file.replace("###CHR###", "*")
-    if len(glob.glob(check_file_path)) == 0:
-        print(f"[ERROR] Custom annotation file does not exist - {file}. Exiting ...")
-        exit(1)
-
-    fields = "%".join(fields)
-
-    custom_line = f"custom file={file},short_name={short_name},format={format},type={type},coords={coords},fields={fields}"
-
-    return custom_line
-
-
-def get_frequency_args(
-    population_data_file: str, species: str, placeholders: dict
-) -> list:
-    """Construct VEP custom arguments for population frequency resources.
-
-    Parses the provided population JSON and constructs custom lines for each population
-    data file.
-
-    Args:
-        population_data_file (str): Path to population JSON file.
-        species (str): Species production name.
-        placeholders (Placeholders): Placeholders instance used to resolve template paths.
-
-    Returns:
-        list: List of custom argument strings to include in VEP config.
-    """
-    with open(population_data_file, "r") as file:
-        population_data = json.load(file)
-
-    possible_placeholders = ["ASSEMBLY_ACC"]
-    frequencies = []
-    for species_patt in population_data:
-        if re.fullmatch(species_patt, species):
-            for population in population_data[species_patt]:
-                for file in population["files"]:
-                    short_name = file["short_name"]
-                    file_location = file["file_location"]
-                    fields = [
-                        field
-                        for pop in file["include_fields"]
-                        for field in list(pop["fields"].values())
-                    ]
-
-                    placeholders.source_text = file_location
-                    for placeholder in possible_placeholders:
-                        placeholders.add_placeholder(placeholder)
-                    placeholders.replace()
-                    file_location = placeholders.source_text
-
-                    frequencies.append(
-                        format_custom_args(
-                            short_name=short_name, file=file_location, fields=fields
-                        )
-                    )
-
-    # Add 1kg population to be included from cache for human GRCh38 and GRCh37
-    if species == "homo_sapiens" or species == "homo_sapiens_37":
-        frequencies.append("af_1kg 1")
-
-    return frequencies
-
-
-def check_plugin_files(plugin: str, files: list, exit_rule: str = "exit") -> bool:
-    """Verify presence of plugin data files.
-
-    Args:
-        plugin (str): Plugin name for logging.
-        files (list): List of file paths to check.
-        exit_rule (str): 'exit' to raise on missing file, 'skip' to return False.
-
-    Returns:
-        bool: True if all files exist, False if skipped due to exit_rule 'skip'.
-
-    Raises:
-        FileNotFoundError: If a required file is missing and exit_rule is 'exit'.
-    """
-    for file in files:
-        if not os.path.isfile(file):
-            if exit_rule == "skip":
-                print(f"[INFO] Cannot get {plugin} data file - {file}. Skipping ...")
-                return False
-
-            raise FileNotFoundError(
-                f"[ERROR] Cannot get {plugin} data file - {file}. Exiting ..."
-            )
-
-    return True
-
-
-def get_plugin_args(
-    plugin: str,
-    version: int,
-    species: str,
-    assembly: str,
-    conservation_data_dir: str = CONSERVATION_DATA_DIR,
-) -> str:
-    """Return plugin configuration line(s) for the requested plugin.
-
-    The returned string is suitable for inclusion as 'plugin <args>' in the VEP config.
-    For some plugins this includes paths to data files.
-
-    Args:
-        plugin (str): Plugin key.
-        version (int): Ensembl release version.
-        species (str): Species production name.
-        assembly (str): Assembly name.
-        conservation_data_dir (str): Directory containing conservation plugin data.
-
-    Returns:
-        str|None: Plugin argument string for inclusion in VEP config, or None to skip plugin.
-    """
-    plugin_data_dir = PLUGIN_DATA_DIR.replace("VERSION", "e" + str(version))
-    if assembly == "GRCh37":
-        plugin_data_dir = plugin_data_dir.replace("grch38", "grch37")
-
-    if plugin == "CADD":
-        # CADD have data v1.7 data file from e113
-        if version < 113:
-            plugin_data_dir = plugin_data_dir.replace(f"{version}", "113")
-
-        if species == "sus_scrofa":
-            snv = os.path.join(plugin_data_dir, f"ALL_pCADD-PHRED-scores.tsv.gz")
-            check_plugin_files(plugin, [snv])
-
-            return f"CADD,{snv}"
-
-        snv = os.path.join(
-            plugin_data_dir, f"CADD_{assembly}_1.7_whole_genome_SNVs.tsv.gz"
-        )
-        indels = os.path.join(plugin_data_dir, f"CADD_{assembly}_1.7_InDels.tsv.gz")
-
-        check_plugin_files(plugin, [snv, indels])
-
-        return f"CADD,{snv},{indels}"
-
-    if plugin == "REVEL":
-        data_file = f"/nfs/production/flicek/ensembl/variation/data/REVEL/2021-may/new_tabbed_revel_{assembly.lower()}.tsv.gz"
-
-        check_plugin_files(plugin, [data_file])
-
-        return f"REVEL,{data_file}"
-
-    if plugin == "SpliceAI":
-        ucsc_assembly = "hg38" if assembly == "GRCh38" else "hg19"
-        snv = os.path.join(
-            plugin_data_dir, f"spliceai_scores.masked.snv.{ucsc_assembly}.vcf.gz"
-        )
-        indels = os.path.join(
-            plugin_data_dir, f"spliceai_scores.masked.indel.{ucsc_assembly}.vcf.gz"
-        )
-
-        check_plugin_files(plugin, [snv, indels])
-
-        return f"SpliceAI,snv={snv},indel={indels}"
-
-    if plugin == "Phenotypes":
-        pl_assembly = f"_{assembly}" if species == "homo_sapiens" else ""
-        file = os.path.join(
-            plugin_data_dir,
-            f"Phenotypes_data_files/Phenotypes.pm_{species}_{version}{pl_assembly}.gvf.gz",
-        )
-
-        if not check_plugin_files(plugin, [file], "skip"):
-            return None
-
-        return f"Phenotypes,file={file},id_match=1,cols=phenotype&source&id&type&clinvar_clin_sig"
-
-    if plugin == "IntAct":
-        mutation_file = os.path.join(plugin_data_dir, "mutations.tsv")
-        mapping_file = os.path.join(plugin_data_dir, "mutation_gc_map.txt.gz")
-
-        check_plugin_files(plugin, [mutation_file, mapping_file])
-
-        return (
-            f"IntAct,mutation_file={mutation_file},mapping_file={mapping_file},pmid=1"
-        )
-
-    if plugin == "AncestralAllele":
-        # TMP - 110 datafile has 109 in the file name
-        pl_version = "109" if assembly == "GRCh38" else "e75"
-        file = os.path.join(
-            plugin_data_dir, f"homo_sapiens_ancestor_{assembly}_{pl_version}.fa.gz"
-        )
-
-        check_plugin_files(plugin, [file])
-
-        return f"AncestralAllele,{file}"
-
-    if plugin == "Conservation":
-        file = os.path.join(
-            conservation_data_dir, f"gerp_conservation_scores.{species}.{assembly}.bw"
-        )
-
-        if not check_plugin_files(plugin, [file], "skip"):
-            return None
-
-        return f"Conservation,{file}"
-
-    if plugin == "MaveDB":
-        file = os.path.join(plugin_data_dir, "MaveDB_variants.tsv.gz")
-
-        if not check_plugin_files(plugin, [file], "skip"):
-            return None
-
-        return f"MaveDB,file={file},cols=MaveDB_score:MaveDB_urn,transcript_match=1"
-
-    if plugin == "AlphaMissense":
-        # Alphamissense do not have data file in e110 directory or below
-        if version < 111:
-            plugin_data_dir = plugin_data_dir.replace(f"{version}", "111")
-        file = os.path.join(plugin_data_dir, "AlphaMissense_hg38.tsv.gz")
-
-        if not check_plugin_files(plugin, [file], "skip"):
-            return None
-
-        return f"AlphaMissense,file={file}"
-
-    if plugin == "ClinPred":
-        # ClinPred do not have data file in e113 directory or below
-        if version < 113:
-            plugin_data_dir = plugin_data_dir.replace(f"{version}", "113")
-        file_name = (
-            "ClinPred_hg38_sorted_tabbed.tsv.gz"
-            if assembly == "GRCh38"
-            else "ClinPred_tabbed.tsv.gz"
-        )
-        file = os.path.join(plugin_data_dir, "ClinPred", file_name)
-
-        if not check_plugin_files(plugin, [file], "skip"):
-            return None
-
-        return f"ClinPred,file={file}"
-
-    # some plugin do not need any arguments, for example - Downstream plugin
-    return plugin
-
-
-def get_plugin_species(plugin: str, repo_dir: str) -> list:
-    """Return list of species supported by a plugin.
-
-    Reads VEP_plugins/plugin_config.txt and returns the 'species' array for the requested plugin.
-
-    Args:
-        plugin (str): Plugin key to look up.
-        repo_dir (str): Path to the repository containing VEP_plugins.
-
-    Returns:
-        list: List of species keys supported by the plugin, or empty list if unspecified.
-
-    Exits:
-        Exits the script if the plugin config file cannot be read or parsed.
-    """
-    plugin_config_file = f"{repo_dir}/VEP_plugins/plugin_config.txt"
-
-    if not os.path.isfile(plugin_config_file):
-        print(
-            f"[ERROR] Plugin config file does not exist - {plugin_config_file}. Exiting ..."
-        )
-        exit(1)
-
-    cmd_generate_plugin_config_json = "use JSON;"
-    cmd_generate_plugin_config_json += f"open IN, '{plugin_config_file}';"
-    cmd_generate_plugin_config_json += "my @content = <IN>;"
-    cmd_generate_plugin_config_json += "close IN;"
-    cmd_generate_plugin_config_json += (
-        "my $VEP_PLUGIN_CONFIG = eval join('', @content);"
-    )
-    cmd_generate_plugin_config_json += "print encode_json($VEP_PLUGIN_CONFIG);"
-
-    process = subprocess.run(
-        ["perl", "-e", cmd_generate_plugin_config_json],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-    if process.returncode != 0:
-        print(
-            f"[ERROR] Cannot read plugin config file - {plugin_config_file}\n{process.stderr.decode()}\nExiting ..."
-        )
-        exit(1)
-
-    plugin_config_json = json.loads(process.stdout)
-    for plugin_config in plugin_config_json["plugins"]:
-        if plugin_config["key"] == plugin:
-            return plugin_config["species"] if "species" in plugin_config else []
-
-    return []
-
-
-def get_plugins(
-    species: str,
-    version: int,
-    assembly: str,
-    repo_dir: str = REPO_DIR,
-    conservation_data_dir: str = CONSERVATION_DATA_DIR,
-) -> list:
-    """Assemble plugin argument strings for the species and version.
-
-    Args:
-        species (str): Species production name.
-        version (int): Ensembl release version.
-        assembly (str): Assembly name.
-        repo_dir (str): Repository directory.
-        conservation_data_dir (str): Conservation plugin data directory.
-
-    Returns:
-        list: List of plugin argument strings to include in the VEP config.
-    """
-    plugins = []
-
-    for plugin in PLUGINS:
-        plugin_species = get_plugin_species(plugin, repo_dir)
-        if len(plugin_species) == 0 or species in plugin_species:
-            plugin_args = get_plugin_args(
-                plugin, version, species, assembly, conservation_data_dir
-            )
-            if plugin_args is not None:
-                plugins.append(plugin_args)
-
-    return plugins
-
-
-def main(args=None):
-    """Generate a VEP configuration file for the specified species/version.
-
-    The function parses inputs, discovers available resources/plugins and writes the final
-    VEP configuration file.
-
-    Args:
-        args (list|None): Optional argument list for testing; if None uses sys.argv.
-
-    Returns:
-        None
-    """
-    args = parse_args(args)
-
-    version = args.version
-    species = args.species
-    assembly = args.assembly
-    genome_uuid = args.genome_uuid or None
-    vep_config = args.vep_config or f"{species}_{assembly}.ini"
-    ini_file = args.ini_file or "DEFAULT.ini"
-    repo_dir = args.repo_dir or REPO_DIR
-
-    # get species division
-    core_server = parse_ini(ini_file, "core")
-    core_db = get_db_name(core_server, args.version, species, type="core")
-    division = args.division or get_division(core_server, core_db)
-
-    # TMP - until we use fasta from new website infra
-    species = "homo_sapiens" if species == "homo_sapiens_37" else species
-
-    if args.cache_dir and args.gff_dir:
-        raise Exception(
-            "[ERROR] Cannot use both cache and gff at the same time, but both given."
-        )
-
-    if args.cache_dir:
-        cache_dir = args.cache_dir
-        cache_version = get_relative_version(version, division)
-        genome_cache_dir = os.path.join(
-            cache_dir, species, f"{cache_version}_{assembly}"
-        )
-        if not os.path.exists(genome_cache_dir):
-            raise FileNotFoundError(
-                f"[ERROR] {genome_cache_dir} directory does not exists, cannot run VEP. Exiting ..."
-            )
-    elif args.gff_dir:
-        gff_dir = args.gff_dir
-        gff = os.path.join(gff_dir, "sorted_genes.gff3.gz")
-        if not os.path.isfile(gff):
-            raise FileNotFoundError(
-                f"[ERROR] No valid GFF file found, cannot run VEP. Exiting ..."
-            )
-
-    fasta_species_name = get_fasta_species_name(species)
-    fasta_dir = args.fasta_dir or FASTA_DIR
-    if args.use_old_infra:
-        fasta = os.path.join(
-            fasta_dir, f"{fasta_species_name}.{assembly}.dna.primary_assembly.fa.gz"
-        )
-        if not os.path.isfile(fasta):
-            fasta = os.path.join(
-                fasta_dir, f"{fasta_species_name}.{assembly}.dna.toplevel.fa.gz"
-            )
-        if not os.path.isfile(fasta):
-            raise FileNotFoundError(
-                f"[ERROR] No valid FASTA file found, cannot run VEP. Exiting ..."
-            )
-    else:
-        fasta = os.path.join(fasta_dir, "unmasked.fa.gz")
-        if not os.path.isfile(fasta):
-            raise FileNotFoundError(
-                f"[ERROR] No valid FASTA file found, cannot run VEP. Exiting ..."
-            )
-
-    conservation_data_dir = args.conservation_data_dir or CONSERVATION_DATA_DIR
-    structural_variant = args.structural_variant
-
-    sift = False
-    if species in SIFT_SPECIES and not structural_variant:
-        sift = True
-
-    polyphen = False
-    if species in POLYPHEN_SPECIES and not structural_variant:
-        polyphen = True
-
-    frequencies = []
-    population_data_file = args.population_data_file or ""
-    if os.path.isfile(population_data_file):
-        placeholders = Placeholders(
-            data={
-                "genome_uuid": genome_uuid,
-                "server": parse_ini(ini_file, "metadata"),
-                "metadata_db": "ensembl_genome_metadata",
-            }
-        )
-        frequencies = get_frequency_args(population_data_file, species, placeholders)
-    else:
-        print(f"[WARNING] Invalid population config file - {population_data_file}")
-
-    plugins = get_plugins(species, version, assembly, repo_dir, conservation_data_dir)
-
-    # write the VEP config file
-    with open(vep_config, "w") as file:
-        file.write("force_overwrite 1\n")
-        file.write(f"fork 2\n")
-        file.write(f"species {species}\n")
-        file.write(f"assembly {assembly}\n")
-        file.write(f"fasta {fasta}\n")
-        file.write("vcf 1\n")
-        file.write("spdi 1\n")
-        file.write("regulatory 1\n")
-        file.write("pubmed 1\n")
-        file.write("var_synonyms 1\n")
-        file.write("variant_class 1\n")
-        file.write("protein 1\n")
-        file.write("transcript_version 1\n")
-
-        if args.cache_dir:
-            file.write(f"cache_version {version}\n")
-            file.write(f"cache {args.cache_dir}\n")
-            file.write("offline 1\n")
-        elif args.gff_dir:
-            file.write(f"gff {gff}\n")
-
-        if sift:
-            file.write(f"sift b\n")
-        if polyphen:
-            file.write(f"polyphen b\n")
-        if frequencies:
-            for frequency in frequencies:
-                file.write(f"{frequency}\n")
-
-        if plugins:
-            file.write(f"dir_plugins {repo_dir}/VEP_plugins\n")
-
-            for plugin in plugins:
-                file.write(f"plugin {plugin}\n")
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/helper.py b/nextflow/vcf_prepper/bin/helper.py
index 29a61dc3..430f5ccc 100755
--- a/nextflow/vcf_prepper/bin/helper.py
+++ b/nextflow/vcf_prepper/bin/helper.py
@@ -646,72 +646,6 @@ def download_file(local_filename: str, url: str) -> int:
     return process.returncode
 
 
-def get_ftp_path(
-    species: str,
-    assembly: str,
-    division: str,
-    version: int,
-    type: str = "cache",
-    mode: str = "local",
-    species_url_name: str = None,
-) -> str:
-    """Construct a local or remote path for various Ensembl resources.
-
-    Args:
-        species (str): Species production name.
-        assembly (str): Assembly name.
-        division (str): Ensembl division.
-        version (int): Release version.
-        type (str): Resource type ('cache', 'fasta', 'conservation').
-        mode (str): 'local' or 'remote' to specify returned path type.
-        species_url_name (str|None): Optional species name used in FASTA filename.
-
-    Returns:
-        str|None: Full path string or None if not available locally.
-    """
-    version = str(version)
-    if species == "homo_sapiens_37":
-        species = "homo_sapiens"
-
-    if mode == "local":
-        base = "/nfs/production/flicek/ensembl/production/ensemblftp"
-    elif mode == "remote" and assembly == "GRCh37":
-        base = "ftp.ensembl.org/pub/grch37"
-    elif mode == "remote" and division == "EnsemblVertebrates":
-        base = "ftp.ensembl.org/pub"
-    else:
-        base = "ftp.ebi.ac.uk/ensemblgenomes/pub"
-
-    release_segment = f"release-{version}"
-
-    division_segment = ""
-    if division != "EnsemblVertebrates" and type != "conservation":
-        division_segment = f"{division[7:].lower()}"
-
-    if type == "cache":
-        prefix = "variation/indexed_vep_cache"
-    elif type == "fasta":
-        prefix = f"fasta/{species}/dna"
-    elif type == "conservation":
-        prefix = "compara/conservation_scores/91_mammals.gerp_conservation_score"
-
-    if type == "cache":
-        file_name = f"{species}_vep_{version}_{assembly}.tar.gz"
-    elif type == "fasta":
-        file_name = f"{species_url_name}.{assembly}.dna.toplevel.fa.gz"
-    elif type == "conservation":
-        file_name = f"gerp_conservation_scores.{species}.{assembly}.bw"
-
-    full_path = os.path.join(base, release_segment, division_segment, prefix, file_name)
-
-    if mode == "local" and os.path.isfile(full_path):
-        return full_path
-    elif mode == "remote":
-        return f"https://{full_path}"
-
-    return None
-
-
 def copyto(src_file: str, dest_file: str) -> int:
     """Copy a file using rsync.
 
diff --git a/nextflow/vcf_prepper/bin/process_cache.py b/nextflow/vcf_prepper/bin/process_cache.py
index 86fb8a4c..a6fff7e0 100755
--- a/nextflow/vcf_prepper/bin/process_cache.py
+++ b/nextflow/vcf_prepper/bin/process_cache.py
@@ -15,17 +15,15 @@
 # limitations under the License.
 
 import sys
-import configparser
 import argparse
 import subprocess
 import os
-import requests
-import shutil
 
 from helper import *
 
-CACHE_DIR = "/nfs/production/flicek/ensembl/variation/data/VEP/tabixconverted"
-
+from ensembl.variation_utils.file_utils import is_bgzip, bgzip_file, ungzip_file
+from ensembl.variation_utils.file_locator import ftp, vep_cache
+from ensembl.variation_utils.clients import core, metadata
 
 def parse_args(args=None):
     """Parse command-line arguments for cache processing.
@@ -39,15 +37,19 @@ def parse_args(args=None):
     """
     parser = argparse.ArgumentParser()
 
-    parser.add_argument(dest="species", type=str, help="species production name")
-    parser.add_argument(dest="assembly", type=str, help="assembly default")
-    parser.add_argument(dest="version", type=int, help="Ensembl release version")
     parser.add_argument(
-        "--division",
-        dest="division",
-        type=str,
+        "--genome_uuid", dest="genome_uuid", type=str, help="Genome uuid"
+    )
+    parser.add_argument("--species", dest="species", type=str, help="species production name")
+    parser.add_argument("--assembly", dest="assembly", type=str, help="assembly default")
+    parser.add_argument("--version", dest="version", type=int, help="Ensembl release version")
+    parser.add_argument("--factory", dest="factory", type=str, help="VEP Cache factory")
+    parser.add_argument(
+        "--cache_dir",
+        dest="cache_dir",
+        nargs="?",
         required=False,
-        help="Ensembl division the species belongs to",
+        help="VEP cache directory",
     )
     parser.add_argument(
         "-I",
@@ -58,13 +60,11 @@ def parse_args(args=None):
         help="full path database configuration file, default - DEFAULT.ini in the same directory.",
     )
     parser.add_argument(
-        "--cache_dir",
-        dest="cache_dir",
-        type=str,
-        required=False,
-        help="VEP cache directory",
+        "--out_dir",
+        dest="out_dir",
+        nargs="?",
+        help="Out directory where processed GFF file will be created",
     )
-    parser.add_argument("--force", dest="force", action="store_true")
 
     return parser.parse_args(args)
 
@@ -107,48 +107,54 @@ def main(args=None):
     species = args.species
     assembly = args.assembly
     version = args.version
+    genome_uuid = args.genome_uuid
+    cache_dir = args.cache_dir
+    out_dir = args.out_dir or os.getcwd()
+    factory = args.factory
     ini_file = args.ini_file or "DEFAULT.ini"
-    core_server = parse_ini(ini_file, "core")
-    core_db = get_db_name(core_server, args.version, species, type="core")
-    division = args.division or get_division(core_server, core_db)
 
-    # TMP - until we use fasta from new website infra
-    cachedir_species_name = "homo_sapiens" if species == "homo_sapiens_37" else species
+    cache_vep_config_file = genome_uuid + ".cache.txt"
 
-    cache_dir = args.cache_dir or CACHE_DIR
-    rl_version = get_relative_version(version, division)
-    genome_cache_dir = os.path.join(
-        cache_dir, cachedir_species_name, f"{rl_version}_{assembly}"
-    )
-    if os.path.exists(genome_cache_dir):
-        if not args.force:
-            print(f"[INFO] {genome_cache_dir} directory exists. Skipping ...")
-            exit(0)
+    if not os.path.isfile(ini_file):
+        raise FileNotFoundError(f"[ERROR] INI file not found - {ini_file}")
+
+    core_db_client = core.CoreDBClient(ini_file=ini_file, species=species, version=version)
+    division = core_db_client.get_division()
+    rl_version = (version - 53) if division != "EnsemblVertebrates" else version
+    if cache_dir:
+        cachedir_species_name = "homo_sapiens" if species == "homo_sapiens_37" else species
+        genome_cache_dir = os.path.join(
+            cache_dir, cachedir_species_name, f"{rl_version}_{assembly}"
+        )
+        if os.path.exists(genome_cache_dir):
+            with open(cache_vep_config_file, "w") as f:
+                f.write(f"cache\t{cache_dir}\n")
+                f.write(f"cache_version\t{rl_version}")
         else:
-            print(
-                f"[INFO] {genome_cache_dir} directory exists. Will be overwritten ..."
+            rel_genome_cache_dir = os.path.join(
+                cachedir_species_name, f"{rl_version}_{assembly}"
             )
-            shutil.rmtree(genome_cache_dir)
+            raise FileNotFoundError(f"[ERROR] {rel_genome_cache_dir} not found in {cache_dir}")
 
-    compressed_cache = get_ftp_path(species, assembly, division, rl_version, "cache")
+    else:
+        cache_locator_factory = vep_cache.VEPCacheLocatorFactory()
+        locator = cache_locator_factory.set_locator(factory)
 
-    if compressed_cache is None:
-        print(
-            f"[INFO] Could not find cache in local ftp directory, will retry using remote FTP"
-        )
-
-        compressed_cache_url = get_ftp_path(
-            species, assembly, division, rl_version, "cache", "remote"
-        )
+        locator.core_db_client = core_db_client
+        source_cache_file = locator.locate_file()
 
-        compressed_cache = os.path.join(cache_dir, compressed_cache_url.split("/")[-1])
-        returncode = download_file(compressed_cache, compressed_cache_url)
-        if returncode != 0:
-            print(f"[ERROR] Could not download cache file - {compressed_cache_url}")
-            exit(1)
+        if not source_cache_file or (source_cache_file and not os.path.isfile(source_cache_file)):
+            raise FileNotFoundError(f"Could not find - {source_cache_file}")
+        else:
+            copied = locator.copy_file(out_dir)
+            if not copied:
+                raise Exception("[ERROR] Copy failed.")
 
-    uncompress_cache(cache_dir, compressed_cache)
+            uncompress_cache(out_dir, source_cache_file)
 
+            with open(cache_vep_config_file, "w") as f:
+                f.write(f"cache\t{out_dir}\n")
+                f.write(f"cache_version\t{rl_version}")
 
 if __name__ == "__main__":
     sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/process_conservation_data.py b/nextflow/vcf_prepper/bin/process_conservation_data.py
deleted file mode 100755
index 0d06c9c2..00000000
--- a/nextflow/vcf_prepper/bin/process_conservation_data.py
+++ /dev/null
@@ -1,137 +0,0 @@
-#!/usr/bin/env python3
-
-# See the NOTICE file distributed with this work for additional information
-# regarding copyright ownership.
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import sys
-import configparser
-import argparse
-import subprocess
-import os
-import requests
-import glob
-import shutil
-
-from helper import *
-
-CONSERVATION_DATA_DIR = "/nfs/production/flicek/ensembl/variation/data/Conservation"
-
-
-def parse_args(args=None):
-    """Parse command-line arguments for conservation data processing.
-
-    Args:
-        args (list|None): Optional argument list for testing.
-
-    Returns:
-        argparse.Namespace: Parsed arguments including species, assembly, version, division,
-            ini_file, conservation_data_dir and force flag.
-    """
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(dest="species", type=str, help="species production name")
-    parser.add_argument(dest="assembly", type=str, help="assembly default")
-    parser.add_argument(dest="version", type=int, help="Ensembl release version")
-    parser.add_argument(
-        "--division",
-        dest="division",
-        type=str,
-        required=False,
-        help="Ensembl division the species belongs to",
-    )
-    parser.add_argument(
-        "-I",
-        "--ini_file",
-        dest="ini_file",
-        type=str,
-        required=False,
-        help="full path database configuration file, default - DEFAULT.ini in the same directory.",
-    )
-    parser.add_argument(
-        "--conservation_data_dir",
-        dest="conservation_data_dir",
-        type=str,
-        required=False,
-        help="Conservation bigwigs directory",
-    )
-    parser.add_argument("--force", dest="force", action="store_true")
-
-    return parser.parse_args(args)
-
-
-def main(args=None):
-    """Main entry point to ensure conservation bigWig data is available.
-
-    Determines the expected conservation bigWig location, attempts to copy from local
-    FTP or download from remote FTP, and honours the 'force' flag to overwrite existing files.
-
-    Args:
-        args (list|None): Optional argument list for testing; if None uses sys.argv.
-
-    Returns:
-        None
-    """
-    args = parse_args(args)
-
-    species = args.species
-    assembly = args.assembly
-    version = args.version
-    ini_file = args.ini_file or "DEFAULT.ini"
-    core_server = parse_ini(ini_file, "core")
-    core_db = get_db_name(core_server, args.version, species, type="core")
-    division = args.division or get_division(core_server, core_db)
-
-    conservation_data_dir = args.conservation_data_dir or CONSERVATION_DATA_DIR
-    conservation_bw = os.path.join(
-        conservation_data_dir, f"gerp_conservation_scores.{species}.{assembly}.bw"
-    )
-    if os.path.isfile(conservation_bw):
-        if not args.force:
-            print(f"[INFO] {conservation_bw} exists. Skipping ...")
-            exit(0)
-        else:
-            print(f"[INFO] {conservation_bw} exists. Will be overwritten ...")
-            os.remove(conservation_bw)
-
-    src_conservation_bw = get_ftp_path(
-        species, assembly, division, version, "conservation"
-    )
-
-    if src_conservation_bw is not None:
-        conservation_bw = os.path.join(
-            conservation_data_dir, os.path.basename(src_conservation_bw)
-        )
-        returncode = copyto(src_conservation_bw, conservation_bw)
-
-    if src_conservation_bw is None or returncode != 0:
-        print(
-            f"[INFO] Failed to copy conservation file - {src_conservation_bw}, will retry using remote FTP"
-        )
-
-        source_conservation_bw_url = get_ftp_path(
-            species, assembly, division, version, "conservation", "remote"
-        )
-
-        conservation_bw = os.path.join(
-            conservation_data_dir, source_conservation_bw_url.split("/")[-1]
-        )
-        returncode = download_file(conservation_bw, source_conservation_bw_url)
-        if returncode != 0:
-            print(
-                f"[INFO] Could not download conservation bw file - {source_conservation_bw_url}, Skipping ..."
-            )
-
-
-if __name__ == "__main__":
-    sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/process_custom_annotations.py b/nextflow/vcf_prepper/bin/process_custom_annotations.py
new file mode 100755
index 00000000..f376c70e
--- /dev/null
+++ b/nextflow/vcf_prepper/bin/process_custom_annotations.py
@@ -0,0 +1,177 @@
+#!/usr/bin/env python3
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import sys
+import argparse
+import importlib
+import os
+import json
+import re
+import glob
+
+from ensembl.variation_utils.vep_config import custom_annotation
+
+
+def parse_args(args=None):
+    """Parse command-line arguments for VEP configuration generation.
+
+    Args:
+        args (list|None): Optional argument list for testing; if None argparse reads sys.argv.
+
+    Returns:
+        argparse.Namespace: Parsed arguments.
+    """
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument(
+        "--genome_uuid", dest="genome_uuid", type=str, help="Genome UUID"
+    )
+    parser.add_argument("--species", dest="species", nargs="?", help="Species production name")
+    parser.add_argument("--assembly", dest="assembly", nargs="?", help="Assembly default")
+    parser.add_argument("--version", dest="version", nargs="?", help="Ensembl release version")
+    parser.add_argument(
+        "--conf",
+        dest="conf",
+        nargs="?",
+        help="",
+    )
+    parser.add_argument(
+        "--population_data_file",
+        dest="population_data_file",
+        type=str,
+        required=False,
+        help="A JSON file containing population information for all species.",
+    )
+    parser.add_argument(
+        "--skip_file_check",
+        dest="skip_file_check",
+        action="store_true",
+        help="Skip checking for file existance",
+    )
+
+    return parser.parse_args(args)
+
+def format_custom_args(
+    file: str,
+    short_name: str,
+    format: str = "vcf",
+    type: str = "exact",
+    coords: int = 0,
+    fields: list = [],
+    skip_file_check: bool = False
+) -> str:
+    """Format a custom annotation argument line for VEP.
+
+    Validates that files matching the file pattern exist (supports placeholder, e.g. - ###CHR###)
+    and returns a single-line 'custom' configuration for the VEP ini.
+
+    Args:
+        file (str): Path or glob pattern for the custom file, may include '###CHR###'.
+        short_name (str): Short name for the custom annotation.
+        format (str): Format of the custom file (default 'vcf').
+        type (str): Matching type (default 'exact').
+        coords (int): Whether coordinates are present (default 0).
+        fields (list): List of field names to include.
+        skip_file_check (bool): Skip checking file existance
+
+    Returns:
+        str: Formatted custom argument line.
+
+    Exits:
+        Exits the script if no file match is found.
+    """
+    check_file_path = file.replace("###CHR###", "*")
+
+    if len(glob.glob(check_file_path)) == 0 and not skip_file_check:
+        raise FileExistsError(f"[ERROR] Custom annotation file does not exist - {file}. Exiting ...")
+
+    fields = "%".join(fields)
+
+    custom_line = f"custom file={file},short_name={short_name},format={format},type={type},coords={coords},fields={fields}"
+
+    return custom_line
+
+def main(args=None):
+    """Generate a VEP configuration file for the specified species/version.
+
+    The function parses inputs, discovers available resources/plugins and writes the final
+    VEP configuration file.
+
+    Args:
+        args (list|None): Optional argument list for testing; if None uses sys.argv.
+
+    Returns:
+        None
+    """
+    args = parse_args(args)
+
+    genome_uuid = args.genome_uuid or None
+    species = args.species
+    assembly = args.assembly
+    version = args.version
+    config = args.conf
+    population_data_file = args.population_data_file
+    skip_file_check = args.skip_file_check
+
+    custom_annotations_config_file = genome_uuid + ".custom_annotations.txt"
+
+    if config is None or not os.path.isfile(config):
+        raise FileNotFoundError("[ERROR] No custom annotation config file provided")
+    
+    with open(config) as f:
+        config_json = json.load(f)
+
+    with open(custom_annotations_config_file, "w") as f:
+
+        for custom_annotation_config in config_json:
+            annotation_type = custom_annotation_config["name"].capitalize()
+            
+            module = importlib.import_module("ensembl.variation_utils.vep_config.custom_annotation")
+            factory_class = getattr(module, f"{annotation_type}ArgsBuilderFactory")
+
+            custom_annotation_builder_factory = factory_class()
+            custom_annotation_builder = custom_annotation_builder_factory.set_builder()
+
+            custom_annotation_builder.population_data_file = population_data_file
+            # TMP - until we use fasta from new website infra
+            custom_annotation_builder.species = "homo_sapiens" if species == "homo_sapiens_37" else species
+            custom_annotation_builder.assembly = assembly
+
+            if not custom_annotation_builder.match():
+                continue
+
+            custom_annotation_args = custom_annotation_builder.get_args()
+
+            for args in custom_annotation_args:
+                # override any custom argument from vep_config.json
+                if "args" in custom_annotation_config:
+                    for arg_type in custom_annotation_config["args"]:
+                        args[arg_type] = custom_annotation_config["args"][arg_type]
+
+                line = format_custom_args(
+                    file = args["file"],
+                    short_name =  args["short_name"],
+                    format = args["format"],
+                    type = args.get("type", "exact"),
+                    coords = args.get("coords", 0),
+                    fields = args.get("fields", []),
+                    skip_file_check = skip_file_check
+                )
+
+                f.write("custom " + line + "\n")
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/process_fasta.py b/nextflow/vcf_prepper/bin/process_fasta.py
index 0941649f..a1b19e0c 100755
--- a/nextflow/vcf_prepper/bin/process_fasta.py
+++ b/nextflow/vcf_prepper/bin/process_fasta.py
@@ -21,15 +21,12 @@
 import glob
 import re
 
-from helper import *
+from ensembl.variation_utils.file_utils import is_bgzip, bgzip_file, ungzip_file
+from ensembl.variation_utils.file_locator import ftp, fasta
+from ensembl.variation_utils.clients import core, metadata
 
-FASTA_DIR = "/nfs/production/flicek/ensembl/variation/data/VEP/fasta"
-FASTA_FTP_BASE_DIR = (
-    "/hps/nobackup/flicek/ensembl/production/ensembl_dumps/ftp_mvp/organisms"
-)
 FASTA_FILE_NAME = "unmasked.fa.gz"
 
-
 def parse_args(args=None):
     """Parse command-line arguments for processing FASTA files.
 
@@ -43,30 +40,30 @@ def parse_args(args=None):
     parser = argparse.ArgumentParser()
 
     parser.add_argument(
-        "--species", dest="species", type=str, help="species production name"
+        "--genome_uuid", dest="genome_uuid", type=str, help="Genome uuid"
     )
     parser.add_argument(
-        "--genome_uuid", dest="genome_uuid", type=str, help="Genome uuid"
+        "--species", dest="species", nargs="?", help="species production name"
+    )
+    parser.add_argument(
+        "--assembly", dest="assembly", nargs="?", help="assembly default"
+    )
+    parser.add_argument(
+        "--version", dest="version", nargs="?", help="Ensembl release version"
     )
     parser.add_argument(
-        "--assembly", dest="assembly", type=str, help="assembly default"
+        "--fasta_file", dest="fasta_file", nargs="?", default=None, required=False, help="FASTA file"
     )
     parser.add_argument(
-        "--version", dest="version", type=int, help="Ensembl release version"
+        "--fasta_dir", dest="fasta_dir", nargs="?", default=None, help="FASTA directory"
     )
+    parser.add_argument("--factory", dest="factory", type=str, help="FASTA factory")
     parser.add_argument(
         "--out_dir",
         dest="out_dir",
-        type=str,
+        nargs="?",
         help="Out directory where processed GFF file will be created",
     )
-    parser.add_argument(
-        "--division",
-        dest="division",
-        type=str,
-        required=False,
-        help="Ensembl division the species belongs to",
-    )
     parser.add_argument(
         "-I",
         "--ini_file",
@@ -75,21 +72,7 @@ def parse_args(args=None):
         required=False,
         help="full path database configuration file, default - DEFAULT.ini in the same directory.",
     )
-    parser.add_argument(
-        "--fasta_dir",
-        dest="fasta_dir",
-        type=str,
-        required=False,
-        help="FASTA directory",
-    )
-    parser.add_argument(
-        "--use_old_infra",
-        dest="use_old_infra",
-        action="store_true",
-        help="Use old infrastructure to get FASTA file",
-    )
-    parser.add_argument("--force", dest="force", action="store_true")
-
+    
     return parser.parse_args(args)
 
 
@@ -154,158 +137,74 @@ def main(args=None):
     """
     args = parse_args(args)
 
+    species = args.species
+    assembly = args.assembly
+    version = args.version
+    genome_uuid = args.genome_uuid
+    fasta_file = args.fasta_file
+    fasta_dir = args.fasta_dir
     out_dir = args.out_dir or os.getcwd()
+    factory = args.factory
     ini_file = args.ini_file or "DEFAULT.ini"
-    fasta_dir = args.fasta_dir or FASTA_DIR
 
-    if args.use_old_infra:
-        species = args.species
-        assembly = args.assembly
-        version = args.version
+    fasta_vep_config_file = genome_uuid + ".fasta.txt"
 
-        if species is None or assembly is None or version is None:
-            raise Exception(
-                "[ERROR] Cannot run in old infra mode, make sure you have provided --species, --assembly and --version"
-            )
+    if fasta_file:
+        if is_bgzip(fasta_file) and (os.path.isfile(fasta_file + ".fai") and os.path.isfile(fasta_file + ".gzi")):
+            with open(fasta_vep_config_file, "w") as f:
+                f.write(f"fasta\t{fasta_file}\n")
+        else:
+            print(f"[ERROR] {fasta_file} either not bgzipped or missing index")
+            exit(1)
 
-        core_server = parse_ini(ini_file, "core")
-        core_db = get_db_name(core_server, args.version, species, type="core")
-        division = args.division or get_division(core_server, core_db)
-        fasta_species_name = get_fasta_species_name(species)
+    elif fasta_dir:
+        filename = FASTA_FILE_NAME
+        if factory == "old":
+            filename = f"{species[0].upper() + species[1:]}.{assembly}.dna.toplevel.fa.gz"
 
-        # TMP - until we use fasta from new website infra
-        if species == "homo_sapiens_37":
-            fasta_species_name = "Homo_sapiens"
+        fasta_file = os.path.join(fasta_dir, filename)
+        if not os.path.isfile(fasta_file):
+            raise FileNotFoundError(f"[ERROR] {filename} not found in {fasta_dir}")
 
-        fasta_glob = os.path.join(
-            fasta_dir, f"{fasta_species_name}.{assembly}.dna.*.fa.gz"
-        )
+        if is_bgzip(fasta_file) and (os.path.isfile(fasta_file + ".fai") or os.path.isfile(fasta_file + ".gzi")):
+            with open(fasta_vep_config_file, "w") as f:
+                f.write(f"fasta\t{fasta_file}\n")
+        else:
+            print(f"[ERROR] {fasta_file} either not bgzipped or missing index")
+            exit(1)
 
-        fasta = None
-        if glob.glob(fasta_glob) and not args.force:
-            print(f"[INFO] {fasta_glob} exists. Skipping ...")
-
-            fasta = os.path.join(
-                fasta_dir, f"{fasta_species_name}.{assembly}.dna.primary_assembly.fa.gz"
-            )
-            if not os.path.isfile(fasta):
-                fasta = os.path.join(
-                    fasta_dir, f"{fasta_species_name}.{assembly}.dna.toplevel.fa.gz"
-                )
-            if not os.path.isfile(fasta):
-                print(f"[ERROR] No valid fasta file found, cannot run VEP. Exiting ...")
-                exit(1)
+    else:
+        if not os.path.isfile(ini_file):
+            raise FileNotFoundError(f"[ERROR] INI file not found - {ini_file}")
+
+        fasta_locator_factory = fasta.FASTALocatorFactory()
+        locator = fasta_locator_factory.set_locator(factory)
+        
+        source_fasta_file = None
+        if isinstance(locator, ftp.OldFTPFileLocator):
+            core_db_client = core.CoreDBClient(ini_file=ini_file, species=species, version=version)
+            locator.core_db_client = core_db_client
+            source_fasta_file = locator.locate_file()
+        else:
+            metadata_client = metadata.MetadataDBClient(ini_file=ini_file)
+            locator.metadata_client = metadata_client
+            source_fasta_file = locator.locate_file(genome_uuid)
+            
+        if not source_fasta_file or (source_fasta_file and not os.path.isfile(source_fasta_file)):
+            raise FileNotFoundError(f"Could not find - {source_fasta_file}")
         else:
-            if glob.glob(fasta_glob):
-                print(f"[INFO] {fasta_glob} exists. Will be overwritten ...")
-                for f in glob.glob(fasta_glob):
-                    os.remove(f)
-
-            rl_version = get_relative_version(version, division)
-            src_compressed_fasta = get_ftp_path(
-                species,
-                assembly,
-                division,
-                rl_version,
-                "fasta",
-                "local",
-                fasta_species_name,
-            )
-
-            if src_compressed_fasta is not None:
-                compressed_fasta = os.path.join(
-                    fasta_dir, os.path.basename(src_compressed_fasta)
-                )
-                returncode = copyto(src_compressed_fasta, compressed_fasta)
-
-            if src_compressed_fasta is None or returncode != 0:
-                print(
-                    f"[INFO] Failed to copy fasta file - {src_compressed_fasta}, will retry using remote FTP"
-                )
-
-                compressed_fasta_url = get_ftp_path(
-                    species,
-                    assembly,
-                    division,
-                    rl_version,
-                    "fasta",
-                    "remote",
-                    fasta_species_name,
-                )
-
-                compressed_fasta = os.path.join(
-                    fasta_dir, compressed_fasta_url.split("/")[-1]
-                )
-                returncode = download_file(compressed_fasta, compressed_fasta_url)
-                if returncode != 0:
-                    print(
-                        f"[ERROR] Could not download fasta file - {compressed_fasta_url}"
-                    )
-                    exit(1)
+            filename = os.path.basename(source_fasta_file)
+            compressed_fasta = os.path.join(out_dir, filename)
+            copied = locator.copy_file(compressed_fasta)
+            if not copied:
+                raise Exception("[ERROR] Copy failed.")
 
             unzipped_fasta = ungzip_file(compressed_fasta)
-            fasta = bgzip_file(unzipped_fasta)
-
-        if fasta is not None:
-            index_fasta(fasta, force=args.force)
-
-    else:
-        metadb_server = parse_ini(ini_file, "metadata")
-        genome_uuid = args.genome_uuid
-
-        if genome_uuid is None:
-            raise Exception(
-                "[ERROR] Cannot run in new infra mode, make sure you have provided --genome_uuid"
-            )
-
-        source_fasta = os.path.join(fasta_dir, FASTA_FILE_NAME)
-
-        if (
-            not os.path.isfile(source_fasta)
-            or not os.path.isfile(source_fasta + ".fai")
-            or not os.path.isfile(source_fasta + ".gzi")
-            or args.force
-        ):
-            scientific_name = get_scientific_name(
-                metadb_server, "ensembl_genome_metadata", genome_uuid
-            ).replace(" ", "_")
-            if scientific_name == "" or scientific_name is None:
-                raise Exception(
-                    f"[ERROR] Could not retrieve scientific name for genome uuid - {genome_uuid}"
-                )
-            scientific_name = re.sub("[^a-zA-Z0-9]+", " ", scientific_name)
-            scientific_name = re.sub(" +", "_", scientific_name)
-            scientific_name = re.sub("^_+|_+$", "", scientific_name)
-            assembly_accession = get_assembly_accession(
-                metadb_server, "ensembl_genome_metadata", genome_uuid
-            )
-            if assembly_accession == "" or assembly_accession is None:
-                raise Exception(
-                    f"[ERROR] Could not retrieve assembly accession for genome uuid - {genome_uuid}"
-                )
-
-            source_fasta = os.path.join(
-                FASTA_FTP_BASE_DIR,
-                scientific_name,
-                assembly_accession,
-                "genome",
-                FASTA_FILE_NAME,
-            )
-
-            if not os.path.isfile(source_fasta):
-                raise FileNotFoundError(f"Could not find - {source_fasta}")
-            else:
-                compressed_fasta = os.path.join(out_dir, FASTA_FILE_NAME)
-                returncode = copyto(source_fasta, compressed_fasta)
-                if returncode != 0:
-                    raise Exception(
-                        f"Failed to copy.\n\tSource - {source_fasta}\n\tTarget - {compressed_fasta}"
-                    )
-
-                unzipped_fasta = ungzip_file(compressed_fasta)
-                bgzipped_fasta = bgzip_file(unzipped_fasta)
-                index_fasta(bgzipped_fasta, force=args.force)
+            bgzipped_fasta = bgzip_file(unzipped_fasta)
+            index_fasta(bgzipped_fasta)
 
+            with open(fasta_vep_config_file, "w") as f:
+                f.write(f"fasta\t{bgzipped_fasta}\n")
 
 if __name__ == "__main__":
     sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/process_gff.py b/nextflow/vcf_prepper/bin/process_gff.py
index b6fa0775..34ebd156 100755
--- a/nextflow/vcf_prepper/bin/process_gff.py
+++ b/nextflow/vcf_prepper/bin/process_gff.py
@@ -18,15 +18,12 @@
 import argparse
 import subprocess
 import os
-import re
 
-from helper import *
-
-GFF_FASTA_BASE_DIR = (
-    "/hps/nobackup/flicek/ensembl/production/ensembl_dumps/ftp_mvp/organisms"
-)
-GFF_FILE_NAME = "sorted_genes.gff3.gz"
+from ensembl.variation_utils.file_utils import is_bgzip, bgzip_file, ungzip_file
+from ensembl.variation_utils.file_locator import gff
+from ensembl.variation_utils.clients import metadata
 
+GFF_FILE_NAME = "genes.gff3.gz"
 
 def parse_args(args=None):
     """Parse command-line arguments for processing a GFF.
@@ -39,14 +36,18 @@ def parse_args(args=None):
             ini_file, gff_dir and force flag.
     """
     parser = argparse.ArgumentParser()
-    parser.add_argument(dest="genome_uuid", type=str, help="Genome uuid")
+    parser.add_argument("--genome_uuid", dest="genome_uuid", type=str, help="Genome uuid")
+    parser.add_argument(
+        "--gff_file", dest="gff_file", nargs="?", default=None, required=False, help="GFF file"
+    )
     parser.add_argument(
-        dest="release_id", type=str, help="Ensembl release id from metadata database"
+        "--gff_dir", dest="gff_dir", nargs="?", default=None, help="GFF directory"
     )
+    parser.add_argument("--factory", dest="factory", type=str, help="GFF factory")
     parser.add_argument(
         "--out_dir",
         dest="out_dir",
-        type=str,
+        nargs="?",
         help="Out directory where processed GFF file will be created",
     )
     parser.add_argument(
@@ -57,20 +58,16 @@ def parse_args(args=None):
         required=False,
         help="Full path database configuration file, default - DEFAULT.ini in the same directory.",
     )
-    parser.add_argument(
-        "--gff_dir", dest="gff_dir", type=str, required=False, help="GFF directory"
-    )
-    parser.add_argument("--force", dest="force", action="store_true")
+    
 
     return parser.parse_args(args)
 
 
-def index_gff(bgzipped_gff: str, force: str = False) -> None:
+def index_gff(bgzipped_gff: str) -> None:
     """Create a CSI index for a bgzipped GFF file using tabix.
 
     Args:
         bgzipped_gff (str): Path to the bgzipped GFF file.
-        force (bool): If False and a .csi exists, skip indexing.
 
     Raises:
         FileNotFoundError: If the GFF file does not exist.
@@ -81,12 +78,6 @@ def index_gff(bgzipped_gff: str, force: str = False) -> None:
             f"Could not run tabix index. File does not exist - {bgzipped_gff}"
         )
 
-    csi = bgzipped_gff + ".csi"
-
-    if os.path.isfile(csi) and not force:
-        print(f"[INFO] {csi} file exist. Skipping ...")
-        return
-
     process = subprocess.run(
         ["tabix", "-f", "-C", bgzipped_gff],
         stdout=subprocess.PIPE,
@@ -142,86 +133,62 @@ def main(args=None):
     args = parse_args(args)
 
     genome_uuid = args.genome_uuid
-    release_id = args.release_id
+    gff_file = args.gff_file
+    gff_dir = args.gff_dir
     out_dir = args.out_dir or os.getcwd()
+    factory = args.factory
     ini_file = args.ini_file or "DEFAULT.ini"
-    gff_dir = args.gff_dir or os.getcwd()
-    metadb_server = parse_ini(ini_file, "metadata")
-
-    source_gff = os.path.join(gff_dir, GFF_FILE_NAME)
-
-    if (
-        not os.path.isfile(source_gff)
-        or not os.path.isfile(source_gff + ".csi")
-        or args.force
-    ):
-        scientific_name = get_scientific_name(
-            metadb_server, "ensembl_genome_metadata", genome_uuid
-        ).replace(" ", "_")
-        if scientific_name == "" or scientific_name is None:
-            raise Exception(
-                f"[ERROR] Could not retrieve scientific name for genome uuid - {genome_uuid}"
-            )
-        scientific_name = re.sub("[^a-zA-Z0-9]+", " ", scientific_name)
-        scientific_name = re.sub(" +", "_", scientific_name)
-        scientific_name = re.sub("^_+|_+$", "", scientific_name)
-        assembly_accession = get_assembly_accession(
-            metadb_server, "ensembl_genome_metadata", genome_uuid
-        )
-        if assembly_accession == "" or assembly_accession is None:
-            raise Exception(
-                f"[ERROR] Could not retrieve assembly accession for genome uuid - {genome_uuid}"
-            )
-        annotation_source = get_dataset_attribute_value(
-            metadb_server,
-            "ensembl_genome_metadata",
-            genome_uuid,
-            release_id,
-            "genebuild.annotation_source",
-        )
-        if annotation_source == "" or annotation_source is None:
-            raise Exception(
-                f"[ERROR] Could not retrieve genebuild annotation source for genome uuid - {genome_uuid} and release id - {release_id}"
-            )
-        annotation_source = annotation_source.lower()
-        last_geneset_update = get_dataset_attribute_value(
-            metadb_server,
-            "ensembl_genome_metadata",
-            genome_uuid,
-            release_id,
-            "genebuild.last_geneset_update",
-        )
-        if last_geneset_update == "" or last_geneset_update is None:
-            raise Exception(
-                f"[ERROR] Could not retrieve last genebuild udpate date for genome uuid - {genome_uuid} and release id - {release_id}"
-            )
-        last_geneset_update = last_geneset_update.replace("-", "_")
-        last_geneset_update = re.sub("[\-\s]", "_", last_geneset_update)
-
-        source_gff = os.path.join(
-            GFF_FASTA_BASE_DIR,
-            scientific_name,
-            assembly_accession,
-            annotation_source,
-            "geneset",
-            last_geneset_update,
-            "genes.gff3.gz",
-        )
 
-        if not os.path.isfile(source_gff):
-            raise FileNotFoundError(f"Could not find - {source_gff}")
+    gff_vep_config_file = genome_uuid + ".gff.txt"
+
+    if gff_file:
+        if is_bgzip(gff_file) and (os.path.isfile(gff_file + ".tbi") or os.path.isfile(gff_file + ".csi")):
+            with open(gff_vep_config_file, "w") as f:
+                f.write(f"gff\t{gff_file}")
         else:
-            compressed_gff = os.path.join(out_dir, "genes.gff3.gz")
-            returncode = copyto(source_gff, compressed_gff)
-            if returncode != 0:
-                raise Exception(
-                    f"Failed to copy.\n\tSource - {source_gff}\n\tTarget - {compressed_gff}"
-                )
+            print(f"[ERROR] {gff_file} either not bgzipped or missing tabix index")
+            exit(1)
+
+    elif gff_dir:
+        gff_file = os.path.join(gff_dir, GFF_FILE_NAME)
+        if not os.path.isfile(gff_file):
+            raise FileNotFoundError(f"[ERROR] {GFF_FILE_NAME} not found in {gff_dir}")
+
+        if is_bgzip(gff_file) and (os.path.isfile(gff_file + ".tbi") or os.path.isfile(gff_file + ".csi")):
+            with open(gff_vep_config_file, "w") as f:
+                f.write(f"gff\t{gff_file}")
+        else:
+            print(f"[ERROR] {gff_file} either not bgzipped or missing tabix index")
+            exit(1)
+
+    else:
+        if not os.path.isfile(ini_file):
+            raise FileNotFoundError(f"[ERROR] INI file not found - {ini_file}")
+
+        gff_locator_factory = gff.GFFLocatorFactory()
+        locator = gff_locator_factory.set_locator(factory)
+        
+        metadata_client = metadata.MetadataDBClient(ini_file=ini_file)
+        locator.metadata_client = metadata_client
+
+        source_gff_file = locator.locate_file(genome_uuid)
+            
+        if not source_gff_file or (source_gff_file and not os.path.isfile(source_gff_file)):
+            raise FileNotFoundError(f"Could not find - {source_gff_file}")
+        else:
+            filename = os.path.basename(source_gff_file)
+            compressed_gff = os.path.join(out_dir, filename)
+            copied = locator.copy_file(compressed_gff)
+            if not copied:
+                raise Exception("[ERROR] Copy failed.")
 
             unzipped_gff = ungzip_file(compressed_gff)
             sorted_gff = sort_gff(unzipped_gff)
             bgzipped_gff = bgzip_file(sorted_gff)
-            index_gff(bgzipped_gff, force=args.force)
+            index_gff(bgzipped_gff)
+
+            with open(gff_vep_config_file, "w") as f:
+                f.write(f"gff\t{bgzipped_gff}")
 
 
 if __name__ == "__main__":
diff --git a/nextflow/vcf_prepper/bin/process_vep_plugins.py b/nextflow/vcf_prepper/bin/process_vep_plugins.py
new file mode 100755
index 00000000..8d0a3fcf
--- /dev/null
+++ b/nextflow/vcf_prepper/bin/process_vep_plugins.py
@@ -0,0 +1,128 @@
+#!/usr/bin/env python3
+
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import sys
+import argparse
+import os
+import json
+
+from ensembl.variation_utils.vep_config import plugin
+
+
+def parse_args(args=None):
+    """Parse command-line arguments for VEP configuration generation.
+
+    Args:
+        args (list|None): Optional argument list for testing; if None argparse reads sys.argv.
+
+    Returns:
+        argparse.Namespace: Parsed arguments.
+    """
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument(
+        "--genome_uuid", dest="genome_uuid", type=str, help="Genome UUID"
+    )
+    parser.add_argument("--species", dest="species", nargs="?", help="Species production name")
+    parser.add_argument("--assembly", dest="assembly", nargs="?", help="Assembly default")
+    parser.add_argument("--version", dest="version", nargs="?", type=int, help="Ensembl release version")
+    parser.add_argument(
+        "--conf",
+        dest="conf",
+        nargs="?",
+        help="VEP plugin configuration file",
+    )
+    parser.add_argument(
+        "--repo_dir",
+        dest="repo_dir",
+        nargs="?",
+        help="",
+    )
+
+    return parser.parse_args(args)
+
+def main(args=None):
+    """Generate a VEP configuration file for the specified species/version.
+
+    The function parses inputs, discovers available resources/plugins and writes the final
+    VEP configuration file.
+
+    Args:
+        args (list|None): Optional argument list for testing; if None uses sys.argv.
+
+    Returns:
+        None
+    """
+    args = parse_args(args)
+
+    genome_uuid = args.genome_uuid or None
+    species = args.species
+    assembly = args.assembly
+    version = args.version
+    config = args.conf
+    repo_dir = args.repo_dir or os.environ["ENSEMBL_ROOT_DIR"]
+
+    plugin_vep_config_file = genome_uuid + ".plugins.txt"
+
+    if config is None or not os.path.isfile(config):
+        raise FileNotFoundError("[ERROR] No plugin config file provided")
+
+    with open(config) as f:
+        config_json = json.load(f)
+
+    # if there is no plugin in config create empty file and exit
+    if not config_json:
+        with open(plugin_vep_config_file, "w") as f:
+            pass
+        
+        print("[INFO] No plugin mentioned in config...")
+        exit(0)
+
+    plugin_builder_factory = plugin.PluginArgsBuilderFactory()
+    plugin_builder = plugin_builder_factory.set_builder()
+
+    # TMP - until we use fasta from new website infra
+    plugin_builder.species = "homo_sapiens" if species == "homo_sapiens_37" else species
+    plugin_builder.assembly = assembly
+    plugin_builder.version = version
+
+    with open(plugin_vep_config_file, "w") as f:
+        f.write(f"dir_plugins\t{repo_dir}/VEP_plugins\n")
+        for plugin_config in config_json:
+            plugin_name = plugin_config["name"]
+            keyed = plugin_config.get("keyed", False)
+
+            if not plugin_builder.match(plugin_name):
+                continue
+
+            plugin_args = plugin_builder.get_args(plugin_name)
+
+            for arg in plugin_config.get("args", []):
+                plugin_args[arg] = plugin_config["args"].get(arg, plugin_args[arg])
+
+            if keyed:
+                f.write(f"plugin\t{plugin_name}," 
+                        + ",".join([f"{k}={v}" for k, v in plugin_args.items()]) 
+                        + "\n"
+                    )
+            else:    
+                f.write(f"plugin\t{plugin_name}," 
+                        + ",".join(plugin_args.values()) 
+                        + "\n"
+                    )
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/nextflow/vcf_prepper/bin/summary_stats.py b/nextflow/vcf_prepper/bin/summary_stats.py
index 764f3edd..fffc0436 100755
--- a/nextflow/vcf_prepper/bin/summary_stats.py
+++ b/nextflow/vcf_prepper/bin/summary_stats.py
@@ -140,36 +140,6 @@ def header_match(want_header: dict, got_header: dict) -> bool:
     )
 
 
-def minimise_allele(ref: str, alts: list) -> str:
-    """Minimise allele representation by trimming a common leading base.
-
-    If all alleles share the same first base, remove it from REF and ALT alleles; an empty
-    allele becomes '-' to preserve representation.
-
-    Args:
-        ref (str): Reference allele.
-        alts (list): List of alternate alleles.
-
-    Returns:
-        tuple: (minimised_ref, minimised_alts) where minimised_alts is a list of strings.
-    """
-    alleles = [ref] + alts
-    first_bases = {allele[0] for allele in alleles}
-
-    if len(first_bases) == 1:
-        ref = ref[1:] or "-"
-
-        temp_alts = []
-        for alt in alts:
-            if "*" in alt:
-                temp_alts.append(alt)
-            else:
-                temp_alts.append(alt[1:] or "-")
-        alts = temp_alts
-
-    return (ref, alts)
-
-
 def main(args=None):
     """Compute and add summary INFO fields to VCF records.
 
@@ -292,7 +262,11 @@ def main(args=None):
     # iterate through the file
     for variant in input_vcf:
         # create minimalized allele order
-        (ref, allele_order) = minimise_allele(variant.REF, variant.ALT)
+        num_of_alleles = len(variant.ALT)
+
+        if "ALLELE_NUM" not in csq_header_idx and num_of_alleles > 1:
+            print("[ERROR] INFO/CSQ must contain ALLELE_NUM for input with multi-allelic variants")
+            exit(1)
 
         items_per_variant = {item: set() for item in PER_VARIANT_FIELDS}
         items_per_allele = {}
@@ -302,9 +276,9 @@ def main(args=None):
         for csq in csqs.split(","):
             csq_values = csq.split("|")
 
-            allele = csq_values[csq_header_idx["Allele"]]
-            if allele not in items_per_allele:
-                items_per_allele[allele] = {item: set() for item in PER_ALLELE_FIELDS}
+            allele_num = csq_values[csq_header_idx.get("ALLELE_NUM", 1)]
+            if allele_num not in items_per_allele:
+                items_per_allele[allele_num] = {item: set() for item in PER_ALLELE_FIELDS}
 
             consequences = csq_values[csq_header_idx["Consequence"]]
             feature_stable_id = csq_values[csq_header_idx["Feature"]]
@@ -322,16 +296,16 @@ def main(args=None):
             if add_transcript_feature:
                 # genes
                 gene = csq_values[csq_header_idx["Gene"]]
-                items_per_allele[allele]["gene"].add(gene)
+                items_per_allele[allele_num]["gene"].add(gene)
 
                 # transcipt consequences
-                items_per_allele[allele]["transcipt_consequence"].add(
+                items_per_allele[allele_num]["transcipt_consequence"].add(
                     f"{feature_stable_id}:{consequences}"
                 )
 
             # regualtory consequences
             if add_regulatory_feature:
-                items_per_allele[allele]["regulatory_consequence"].add(
+                items_per_allele[allele_num]["regulatory_consequence"].add(
                     f"{feature_stable_id}:{consequences}"
                 )
 
@@ -346,11 +320,11 @@ def main(args=None):
 
                     (name, source, feature) = pheno_per_allele_fields
                     if feature.startswith("ENS"):
-                        items_per_allele[allele]["gene_phenotype"].add(
+                        items_per_allele[allele_num]["gene_phenotype"].add(
                             f"{name}:{source}:{feature}"
                         )
                     else:
-                        items_per_allele[allele]["variant_phenotype"].add(
+                        items_per_allele[allele_num]["variant_phenotype"].add(
                             f"{name}:{source}:{feature}"
                         )
 
@@ -422,14 +396,16 @@ def main(args=None):
                     exit(1)
 
                 if len(frequencies) == 1:
-                    items_per_allele[allele]["frequency"] = frequencies[0]
+                    items_per_allele[allele_num]["frequency"] = frequencies[0]
 
         # create summary info for per allele fields
         for field in PER_ALLELE_FIELDS:
             field_nums = []
-            for allele in allele_order:
-                if allele in items_per_allele and field in items_per_allele[allele]:
-                    field_len = len(items_per_allele[allele][field])
+            for allele_num in range(1, num_of_alleles + 1):
+                allele_num = str(allele_num)
+
+                if allele_num in items_per_allele and field in items_per_allele[allele_num]:
+                    field_len = len(items_per_allele[allele_num][field])
                     if field_len > 0:
                         field_nums.append(str(field_len))
 
@@ -438,9 +414,11 @@ def main(args=None):
 
         # create summary info for frequency
         field_vals = []
-        for allele in allele_order:
-            if allele in items_per_allele and "frequency" in items_per_allele[allele]:
-                field_vals.append(items_per_allele[allele]["frequency"])
+        for allele_num in range(1, num_of_alleles + 1):
+            allele_num = str(allele_num)
+
+            if allele_num in items_per_allele and "frequency" in items_per_allele[allele_num]:
+                field_vals.append(items_per_allele[allele_num]["frequency"])
             else:
                 field_vals.append(".")
 
@@ -460,4 +438,4 @@ def main(args=None):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/bin/update_fields.py b/nextflow/vcf_prepper/bin/update_fields.py
index ce7119ee..9bdb766a 100755
--- a/nextflow/vcf_prepper/bin/update_fields.py
+++ b/nextflow/vcf_prepper/bin/update_fields.py
@@ -22,10 +22,11 @@
 
 from helper import *
 
-META = """##fileformat=VCFv4.2
+META = """##fileformat=VCFv4.4
 ##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of the variation data">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
 ##INFO=<ID=SVLEN,Number=.,Type=String,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">
 """
 HEADER = """#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
 """
@@ -234,11 +235,10 @@ def main(args=None):
                         break
             info_fields = f"SOURCE={variant_source}"
 
-            if variant.INFO.get("SVLEN"):
-                info_fields += f";SVLEN={variant.INFO['SVLEN']}"
-
-            if variant.INFO.get("END"):
-                info_fields += f";END={variant.INFO['END']}"
+            retainable_info = ["SVLEN", "END", "NODEID"]
+            for info_field in retainable_info:
+                if variant.INFO.get(info_field):
+                    info_fields += f";{info_field}={variant.INFO[info_field]}"
 
             o_file.write(
                 "\t".join(
@@ -267,4 +267,4 @@ def main(args=None):
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/bin/vcf_to_bed b/nextflow/vcf_prepper/bin/vcf_to_bed
index a8c62063..f46b759b 100755
Binary files a/nextflow/vcf_prepper/bin/vcf_to_bed and b/nextflow/vcf_prepper/bin/vcf_to_bed differ
diff --git a/nextflow/vcf_prepper/cpanfile b/nextflow/vcf_prepper/cpanfile
new file mode 100644
index 00000000..f54690d5
--- /dev/null
+++ b/nextflow/vcf_prepper/cpanfile
@@ -0,0 +1 @@
+requires 'JSON';
diff --git a/nextflow/vcf_prepper/lib/WorkflowMain.groovy b/nextflow/vcf_prepper/lib/WorkflowMain.groovy
index bd193aff..36b75aba 100755
--- a/nextflow/vcf_prepper/lib/WorkflowMain.groovy
+++ b/nextflow/vcf_prepper/lib/WorkflowMain.groovy
@@ -53,4 +53,12 @@ class WorkflowMain {
         Nextflow.file("${params.output_dir}/api").mkdirs()
         Nextflow.file("${params.output_dir}/tracks").mkdirs()
     }
+}
+
+class RemoteURL {
+    RemoteURL(String url){
+        this.url = url
+    }
+
+    
 }
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/main.nf b/nextflow/vcf_prepper/main.nf
index aab3cb57..8ed35f43 100755
--- a/nextflow/vcf_prepper/main.nf
+++ b/nextflow/vcf_prepper/main.nf
@@ -13,28 +13,207 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
-include { VCF_PREPPER } from "./workflows/vcf_prepper.nf"
 
-WorkflowMain.initialise(workflow, params, log)
+include { VCF_PREPPER } from "./workflows/vcf_prepper"
+include { PREPARE_GENOME } from "./subworkflows/local/prepare_genome"
 
 workflow {
-  VCF_PREPPER()
+    initialise(params)
+
+    def input_config = new groovy.json.JsonSlurper().parse(file(params.input_config))
+	vep_config = process_vep_config(params)
+
+    def genome_map = genome_map_from_input_config(input_config)
+    def ch_vcf_list = get_vcf_channel_list(input_config, genome_map)
+
+    PREPARE_GENOME(
+        channel.fromList(genome_map.values()),
+        params.version,
+        params.ini_file
+    )
+
+    VCF_PREPPER(
+        channel.fromList(genome_map.values()),
+        channel.fromList(ch_vcf_list),
+        vep_config.annotation_source.fasta,
+        vep_config.annotation_source.gff,
+        vep_config.annotation_source.cache,
+        vep_config.default_options,
+        vep_config.plugins,
+        vep_config.custom_annotaions,
+        PREPARE_GENOME.out.synonym_file,
+        PREPARE_GENOME.out.chrom_sizes_file,
+        params.ini_file,
+        params.structural_variant,
+        params.version,
+        params.release_id,
+        params.repo_dir,
+        params.population_data_file,
+        params.skip_vep,
+        params.skip_tracks,
+        params.skip_stats,
+		params.bed_fields
+    )
+
+    // Print summary
+    workflow.onComplete {
+        println(
+            workflow.success
+                ? """
+            Workflow summary
+            ----------------
+            Completed at: ${workflow.complete}
+            Duration    : ${workflow.duration}
+            Success     : ${workflow.success}
+            workDir     : ${workflow.workDir}
+            exit status : ${workflow.exitStatus}
+            """
+                : """
+            Failed: ${workflow.errorReport}
+            exit status : ${workflow.exitStatus}
+            """
+        )
+    }
+}
+
+def initialise(params) {
+    // Check proper directory paths have been provided has been provided
+    if (!params.output_dir) {
+        error("Please provide a directory path to create output files e.g. '--output_dir OUTPUT_DIR'")
+    }
+
+    if (!params.temp_dir) {
+        error("Please provide a directory path to create tmp files e.g. '--temp_dir TMP_DIR'")
+    }
+
+    if (!nextflow.Nextflow.file(params.output_dir).exists()) {
+        log.warn("output directory path does not exist - ${params.output_dir}, creating ...")
+        nextflow.Nextflow.file(params.output_dir).mkdirs()
+    }
+
+    if (!nextflow.Nextflow.file(params.temp_dir).exists()) {
+        log.warn("tmp directory path does not exist - ${params.temp_dir}, creating ...")
+        nextflow.Nextflow.file(params.temp_dir).mkdirs()
+    }
+
+    // Create output directory structure
+    nextflow.Nextflow.file("${params.output_dir}/api").mkdirs()
+    nextflow.Nextflow.file("${params.output_dir}/tracks").mkdirs()
 }
 
-// Print summary
-workflow.onComplete {
-  println ( workflow.success ? """
-        Workflow summary
-        ----------------
-        Completed at: ${workflow.complete}
-        Duration    : ${workflow.duration}
-        Success     : ${workflow.success}
-        workDir     : ${workflow.workDir}
-        exit status : ${workflow.exitStatus}
-        """ : """
-        Failed: ${workflow.errorReport}
-        exit status : ${workflow.exitStatus}
-        """
-  )
-}
\ No newline at end of file
+def process_vep_config(params) {
+	def vep_config = [:]
+
+	if (params.vep_config && file(params.vep_config).exists()) {
+		vep_config = new groovy.json.JsonSlurper().parse(file(params.vep_config))
+	}
+
+	if (! vep_config.annotation_source.cache) {
+		log.warn("No VEP cache config found for VEP, disabling...")
+		vep_config.annotation_source.cache = [
+			'active': false
+		]
+	}
+
+	if (! vep_config.annotation_source.gff) {
+		log.warn("No GFF config found for VEP, disabling...")
+		vep_config.annotation_source.gff = [
+			'active': false
+		]
+	}
+
+	if (! vep_config.annotation_source.fasta) {
+		log.warn("No FASTA config found for VEP, enabling...")
+		vep_config.annotation_source.fasta = [
+			'active': true
+		]
+	}
+
+	if (
+			(! vep_config.annotation_source.cache.active) 
+			&& (! vep_config.annotation_source.gff.active) 
+			&& (! params.skip_vep)
+	) {
+		error("Both VEP cache and GFF cannot be disabled when --skip_vep is not set")
+	}
+
+    if (! vep_config.default_options) {
+		log.warn("No default option set for VEP config, VEP job might fail...")
+        vep_config.default_options = [:]
+    }
+
+    if (! vep_config.plugins) {
+        vep_config.plugins = [:]
+    }
+
+    if (! vep_config.custom_annotaions) {
+        vep_config.custom_annotaions = [:]
+    }
+
+	return vep_config
+}
+
+def genome_map_from_input_config(input_config) {
+    def genome_meta = [:]
+
+    def genomes = input_config.keySet()
+    genomes.each { genome ->
+        def source_data = input_config.get(genome)
+
+        source_data.each { source_datum ->
+            def genome_uuid = source_datum.genome_uuid
+            genome_meta[genome_uuid] = [:]
+
+            genome_meta[genome_uuid].genome_uuid = genome_uuid
+            genome_meta[genome_uuid].genome = genome
+            genome_meta[genome_uuid].species = source_datum.species
+            genome_meta[genome_uuid].assembly = source_datum.assembly
+
+            def genome_temp_dir = "${params.temp_dir}/${genome_uuid}"
+            genome_meta[genome_uuid].genome_temp_dir = genome_temp_dir
+            genome_meta[genome_uuid].genome_api_outdir = "${params.output_dir}/api/${genome_uuid}"
+            genome_meta[genome_uuid].genome_tracks_outdir = "${params.output_dir}/tracks/${genome_uuid}"
+
+            genome_meta[genome_uuid].synonym_file = "${genome_temp_dir}/${genome}.synonyms"
+            genome_meta[genome_uuid].chrom_sizes_file = "${genome_temp_dir}/${genome}.chrom.sizes"
+        }
+    }
+
+    return genome_meta
+}
+
+def get_vcf_channel_list(input_config, genome_map) {
+    def ch_vcf_list = []
+
+    def genomes = input_config.keySet()
+    genomes.each { genome ->
+        def source_data = input_config.get(genome)
+        def multiple_source = source_data.size() > 1 ? true : false
+
+        source_data.each { source_datum ->
+            def vcf = source_datum.file_location
+            def genome_uuid = source_datum.genome_uuid
+
+            def genome_meta = genome_map.get(genome_uuid)
+
+            def file_meta = [:]
+            file_meta.source = source_datum.source_name.replace(" ", "_")
+            file_meta.file_type = source_datum.file_type
+            file_meta.multiple_source = multiple_source
+
+            // replace whitespace and / character which causes issue in file name
+            file_meta.source = file_meta.source.replace(" ", "%20")
+            file_meta.source = file_meta.source.replace("/", "%2F")
+
+            // if source is MULTIPLE there are multiple sources; they must be listed  in sources field in the input config
+            if (file_meta.source == "MULTIPLE") {
+                file_meta.sources = source_data.sources.join(",")
+                file_meta.sources = file_meta.sources.replaceAll(" ", "%20")
+            }
+
+            ch_vcf_list.add([genome_meta, file_meta, vcf])
+        }
+    }
+
+    return ch_vcf_list
+}
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_bigbed.nf b/nextflow/vcf_prepper/modules/local/bed_to_bigbed.nf
deleted file mode 100755
index 0d310ba5..00000000
--- a/nextflow/vcf_prepper/modules/local/bed_to_bigbed.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-
-process BED_TO_BIGBED {
-  label 'process_high'
-  
-  input: 
-  tuple val(meta), path(bed)
-  
-  output:
-  path "variant-${source}-details.bb"
-  
-  shell:
-  source = meta.source.toLowerCase()
-  output_bb = "${meta.genome_tracks_outdir}/variant-${source}-details.bb"
-  chrom_sizes = meta.chrom_sizes
-  // structural variant has extent as 10th column
-  type = params.structural_variant ? "-type=bed3+7" : "-type=bed3+6"
-  
-  '''
-  bedToBigBed !{type} !{bed} !{chrom_sizes} !{output_bb}
-  ln -sf !{output_bb} "variant-!{source}-details.bb"
-  
-  # temp: for one source we create symlink for focus if only one source present
-  if [[ ! !{meta.multiple_source} ]]
-  then
-    cd !{meta.genome_tracks_outdir}
-    ln -sf variant-!{source}-details.bb variant-details.bb
-  fi
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_bigbed/main.nf b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/main.nf
new file mode 100755
index 00000000..7e75e1e4
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/main.nf
@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+process BED_TO_BIGBED {
+	input:
+	tuple val(genome_meta), val(file_meta), path(bed)
+	path bed_fields
+
+	output:
+	path "variant-${source}-details.bb"
+
+	script:
+	source = file_meta.source.toLowerCase()
+	output_bb = "${genome_meta.genome_tracks_outdir}/variant-${source}-details.bb"
+	chrom_sizes = genome_meta.chrom_sizes_file
+	bed_fields = bed_fields
+
+	"""
+	total_fields=\$(cat ${bed_fields} | jq .fields | jq length)
+	extra_fields=\$((total_fields-3))
+	if [ "\${extra_fields}" -lt "0" ]
+	then
+		echo "Extra fields cannot be less than 0"
+		exit 1
+	fi
+
+	type="-type=bed3+\${extra_fields}"
+	bedToBigBed \${type} ${bed} ${chrom_sizes} ${output_bb}
+	ln -sf ${output_bb} "variant-${source}-details.bb"
+	
+	# temp: for one source we create symlink for focus if only one source present
+	if [[ "${file_meta.multiple_source}" == "false" ]]
+	then
+		cd ${genome_meta.genome_tracks_outdir}
+		ln -sf variant-${source}-details.bb variant-details.bb
+	fi
+  	"""
+}
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test
new file mode 100644
index 00000000..7f97924a
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test
@@ -0,0 +1,60 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test Process BED_TO_BIGBED"
+    script "../main.nf"
+    process "BED_TO_BIGBED"
+
+    test("bed_to_bigbed") {
+
+        when {
+            process {
+                """
+				// use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+                
+				genome_meta = [:]
+				genome_meta["chrom_sizes_file"] = file("${projectDir}/tests/testdata/homo_sapiens_GRCh38.chrom.sizes")
+				genome_meta["genome_tracks_outdir"] = tmp_dir
+
+				file_meta = [:]
+                file_meta["source"] = "test"
+                file_meta["multiple_source"] = false
+
+				input[0] = tuple(genome_meta, file_meta, file("${moduleDir}/tests/testdata/short_variants.bed"))
+				input[1] = file("${projectDir}/assets/short_variant_bedfields.json")
+                """
+            }
+        }
+
+        then {
+            assert process.success 
+            assert snapshot(process.out).match()
+            
+            // the output is generated at the genome tracks dir
+			// assert for single source we symlink the focus track
+            def tmp_dir = "${moduleDir}/tests/temp"
+			assert file(tmp_dir + "/variant-test-details.bb").exists()
+			assert file(tmp_dir + "/variant-details.bb").exists()
+			assert file(tmp_dir + "/variant-details.bb").getCanonicalPath() == 
+				(projectDir + "/modules/local/bed_to_bigbed/tests/temp/variant-test-details.bb")
+		}
+    }
+}
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test.snap
new file mode 100644
index 00000000..9e3f20fa
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "bed_to_bigbed": {
+        "content": [
+            {
+                "0": [
+                    "variant-test-details.bb:md5,f61c5487148da056b9b479edf64b161b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-12-24T20:51:40.096881"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/testdata/short_variants.bed b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/testdata/short_variants.bed
new file mode 100644
index 00000000..542e11d9
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_bigbed/tests/testdata/short_variants.bed
@@ -0,0 +1,5 @@
+1	230710046	230710047	rs878890662	indel	CCA	CT	3	frameshift_variant
+1	230710047	230710047	rs11568053	SNV	C	T	1	missense_variant
+1	230710048	230710048	rs699	SNV	A	G	1	missense_variant
+2	148468565	148468565	rs1574458957	SNV	C	T	1	missense_variant
+2	148468576	148468576	rs747595019	SNV	A	G	2	synonymous_variant
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_wig.nf b/nextflow/vcf_prepper/modules/local/bed_to_wig/main.nf
similarity index 66%
rename from nextflow/vcf_prepper/modules/local/bed_to_wig.nf
rename to nextflow/vcf_prepper/modules/local/bed_to_wig/main.nf
index 13ae1c1f..2471214e 100755
--- a/nextflow/vcf_prepper/modules/local/bed_to_wig.nf
+++ b/nextflow/vcf_prepper/modules/local/bed_to_wig/main.nf
@@ -17,21 +17,20 @@
  */
 
 process BED_TO_WIG {
-  input: 
-  tuple val(meta), path(bed)
-  
-  output:
-  tuple val(meta), path(output_wig)
-  
-  memory  { (bed.size() * 4.B + 8.GB) * task.attempt }
-  time    { 48.hour * task.attempt }
-  afterScript 'rm all.bed'
-  
-  shell:
-  source = meta.source.toLowerCase()
-  output_wig = "variant-${source}-summary.wig"
-  
-  '''
-  bed_to_wig !{bed} !{output_wig}
-  '''
+	memory { (bed.size() * 4.B + 8.GB) * task.attempt }
+	time { 48.hour * task.attempt }
+
+	input:
+	tuple val(genome_meta), val(file_meta), path(bed)
+
+	output:
+	tuple val(genome_meta), val(file_meta), path(output_wig)
+
+	script:
+	source = file_meta.source.toLowerCase()
+	output_wig = "variant-${source}-summary.wig"
+
+	"""
+	bed_to_wig ${bed} ${output_wig}
+	"""
 }
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test
new file mode 100644
index 00000000..ddc62920
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test
@@ -0,0 +1,43 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test Process BED_TO_WIG"
+    script "../main.nf"
+    process "BED_TO_WIG"
+
+    test("bed_to_wig") {
+
+        when {
+            process {
+                """
+				genome_meta = [:]
+				file_meta = [:]
+                file_meta["source"] = "test"
+
+				input[0] = tuple(genome_meta, file_meta, file("${moduleDir}/tests/testdata/short_variants.bed"))
+                """
+            }
+        }
+
+        then {
+            assert process.success 
+            assert snapshot(process.out).match()
+		}
+    }
+}
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test.snap
new file mode 100644
index 00000000..be791763
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/main.nf.test.snap
@@ -0,0 +1,24 @@
+{
+    "bed_to_wig": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            "source": "test"
+                        },
+                        "variant-test-summary.wig:md5,eca610f2590fd84ebaa23df5d87b2218"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-03T11:35:22.599899"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/testdata/short_variants.bed b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/testdata/short_variants.bed
new file mode 100644
index 00000000..90a6c69b
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/bed_to_wig/tests/testdata/short_variants.bed
@@ -0,0 +1,5 @@
+1 99 100 rs878890662 indel CCA CT 3 frameshift_variant
+1 101 101 rs11568053 SNV C T 1 missense_variant
+1 110 110 rs699 SNV A G 1 missense_variant
+2 399 399 rs1574458957 SNV C T 1 missense_variant
+2 400 400 rs747595019 SNV A G 2 synonymous_variant
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/concat_beds.nf b/nextflow/vcf_prepper/modules/local/concat_beds/main.nf
similarity index 61%
rename from nextflow/vcf_prepper/modules/local/concat_beds.nf
rename to nextflow/vcf_prepper/modules/local/concat_beds/main.nf
index dfbe5615..11524265 100755
--- a/nextflow/vcf_prepper/modules/local/concat_beds.nf
+++ b/nextflow/vcf_prepper/modules/local/concat_beds/main.nf
@@ -15,30 +15,29 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process CONCAT_BEDS {
-  label 'process_high'
-  
-  input: 
-  tuple val(meta), path(bed_files)
-  
-  output: 
-  tuple val(meta), path(output_bed)
-  
-  afterScript 'rm all.bed'
-  
-  shell:
-  source = meta.source
-  output_bed =  "variant-${source}.bed"
-  temp_dir = "tmp"
-    
-  '''
-  # tmp directory for sorting big files
-  mkdir -p !{temp_dir}
-
-  cat !{bed_files} > all.bed
-  LC_COLLATE=C sort -T !{temp_dir} -S1G -k1,1 -k2,2n all.bed > !{output_bed}
-
-  rm -r !{temp_dir}
-  '''
+	label 'process_high'
+
+	input:
+	tuple val(genome_meta), val(file_meta), path(bed_files)
+
+	output:
+	tuple val(genome_meta), val(file_meta), path(output_bed)
+
+	script:
+	source = file_meta.source
+	output_bed = "variant-${source}.bed"
+	temp_dir = "tmp"
+
+	"""
+	# tmp directory for sorting big files
+	mkdir -p ${temp_dir}
+
+	cat ${bed_files} > all.bed
+	LC_COLLATE=C sort -T ${temp_dir} -S1G -k1,1 -k2,2n all.bed > ${output_bed}
+
+	rm -r ${temp_dir}
+    rm all.bed
+	"""
 }
diff --git a/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test
new file mode 100644
index 00000000..c44c30b8
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test
@@ -0,0 +1,52 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test Process CONCAT_BEDS"
+    script "../main.nf"
+    process "CONCAT_BEDS"
+
+    test("concat_beds") {
+
+        when {
+            process {
+                """
+                genoem_meta = [:]
+                file_meta = [:]
+				file_meta["source"] = "test"
+                
+				input[0] = tuple(genoem_meta, file_meta, file("${moduleDir}/tests/testdata/test_bed*.bed"))
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+            
+            // assert the content of the output file
+            def output_file = file(process.out.get(0).get(0).get(2))
+            def lines = output_file.readLines()
+            assert lines.size() == 5
+
+			// asssert temp and all.bed files are deleted
+			assert ! file(workDir + "/all.bed").exists()
+			assert ! file(workDir + "/tmp").exists()
+		}
+    }
+}
diff --git a/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test.snap
new file mode 100644
index 00000000..e2ebfdad
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/concat_beds/tests/main.nf.test.snap
@@ -0,0 +1,24 @@
+{
+    "concat_beds": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            "source": "test"
+                        },
+                        "variant-test.bed:md5,60e90d0f0fcaf973f97124d380334ed2"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-03T11:28:19.819777"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_1.bed b/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_1.bed
new file mode 100644
index 00000000..ce0e6218
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_1.bed
@@ -0,0 +1,3 @@
+1 230710047 230710046 rs878890662 indel CCA CT 3 frameshift_variant
+1 230710047 230710047 rs11568053 SNV C T 1 missense_variant
+1 230710048 230710048 rs699 SNV A G 1 missense_variant
diff --git a/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_2.bed b/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_2.bed
new file mode 100644
index 00000000..e36a6be4
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/concat_beds/tests/testdata/test_bed_2.bed
@@ -0,0 +1,2 @@
+2 148468565 148468565 rs1574458957 SNV C T 1 missense_variant
+2 148468576 148468576 rs747595019 SNV A G 2 synonymous_variant
diff --git a/nextflow/vcf_prepper/modules/local/count_vcf_variant.nf b/nextflow/vcf_prepper/modules/local/count_vcf_variant/main.nf
similarity index 72%
rename from nextflow/vcf_prepper/modules/local/count_vcf_variant.nf
rename to nextflow/vcf_prepper/modules/local/count_vcf_variant/main.nf
index b56a2d8f..ac21d6cd 100755
--- a/nextflow/vcf_prepper/modules/local/count_vcf_variant.nf
+++ b/nextflow/vcf_prepper/modules/local/count_vcf_variant/main.nf
@@ -15,18 +15,25 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process COUNT_VCF_VARIANT {
-    label 'bcftools'
+	label 'bcftools'
 
-    input:
-    tuple val(meta), val(vcf), val(vcf_index)
+	input:
+	tuple val(genome_meta), 
+		val(file_meta),
+		val(vcf), 
+		val(vcf_index)
 
-    output:
-    tuple val(meta), val(vcf), val(vcf_index), env(count)
+	output:
+	tuple val(genome_meta), 
+		val(file_meta),
+		val(vcf), 
+		val(vcf_index), 
+		env(count)
 
-    shell:
-    '''
-    count=$(bcftools index --nrecords !{vcf})
-    '''
-}
\ No newline at end of file
+	script:
+	"""
+    count=\$(bcftools index --nrecords ${vcf})
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/main.nf.test
new file mode 100644
index 00000000..fb736627
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/main.nf.test
@@ -0,0 +1,41 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process COUNT_VCF_VARIANT"
+    script "../main.nf"
+    process "COUNT_VCF_VARIANT"
+
+    test("count") {
+
+        when {
+            process {
+                """
+				vcf = file("${moduleDir}/tests/testdata/test.vcf.gz")
+				vcf_index = file("${moduleDir}/tests/testdata/test.vcf.gz.csi")
+                input[0] = tuple([:], [:], vcf, vcf_index)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.get(0).get(0).get(4) == '1'
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/data/test_runvep.vcf.gz b/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/testdata/test.vcf.gz
similarity index 100%
rename from nextflow/vcf_prepper/tests/data/test_runvep.vcf.gz
rename to nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/testdata/test.vcf.gz
diff --git a/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..48392c5e
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/count_vcf_variant/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/modules/local/create_rank_file.nf b/nextflow/vcf_prepper/modules/local/create_rank_file/main.nf
similarity index 77%
rename from nextflow/vcf_prepper/modules/local/create_rank_file.nf
rename to nextflow/vcf_prepper/modules/local/create_rank_file/main.nf
index 098de1b1..f15b8d4b 100755
--- a/nextflow/vcf_prepper/modules/local/create_rank_file.nf
+++ b/nextflow/vcf_prepper/modules/local/create_rank_file/main.nf
@@ -17,20 +17,20 @@
  */
 
 process CREATE_RANK_FILE {
-  label 'process_low'
+	label 'process_low'
 
-  input:
-  val rank_file
-  
-  output: 
-  val rank_file
-  
-  shell:
-  '''
-  if [[ -f !{rank_file} ]]; then
-    rm !{rank_file}
-  fi
-  
-  generate_consequence_rank.pl -o !{rank_file}
-  '''
+	input:
+	val rank_file
+
+	output:
+	val rank_file
+
+	script:
+	"""
+	if [[ -f ${rank_file} ]]; then
+		rm ${rank_file}
+	fi
+	
+	generate_consequence_rank.pl -o ${rank_file}
+	"""
 }
diff --git a/nextflow/vcf_prepper/modules/local/create_rank_file/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/create_rank_file/tests/main.nf.test
new file mode 100644
index 00000000..078a57c6
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/create_rank_file/tests/main.nf.test
@@ -0,0 +1,52 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process CREATE_RANK_FILE"
+    script "../main.nf"
+    process "CREATE_RANK_FILE"
+
+    test("create_rank_file") {
+
+        when {
+            process {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                input[0] = tmp_dir + "/consequence_rank.json"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            def rank_file = "${moduleDir}/tests/temp/consequence_rank.json"
+            assert file(rank_file).exists()
+
+			// check some values
+            assert path(rank_file).json.missense_variant == "13"
+            assert path(rank_file).json.stop_lost == "6"
+            assert path(rank_file).json.upstream_gene_variant == "32"
+            assert path(rank_file).json.frameshift_variant == "5"
+			assert path(rank_file).json.splice_donor_5th_base_variant == "15"
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/main.nf b/nextflow/vcf_prepper/modules/local/format_vcf/main.nf
new file mode 100644
index 00000000..a8b2db39
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/format_vcf/main.nf
@@ -0,0 +1,70 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+process FORMAT_VCF {
+    memory { (vcf.size() * 16.B + 2.GB) * task.attempt }
+
+    input:
+    tuple val(genome_meta), 
+        val(file_meta),
+        path(vcf),
+        path(vcf_index)
+
+    output:
+    tuple val(genome_meta), 
+		val(file_meta),
+		path(output_file), 
+		path("${output_file}.csi")
+
+    script:
+    output_file =  "FORMATTED-" + genome_meta.genome + "-" + vcf.baseName + ".vcf.gz"
+    chrom_sizes = genome_meta.chrom_sizes_file
+    remove_nonunique_ids = params.remove_nonunique_ids ? "--remove_nonunique_ids" : ""
+    remove_patch_regions = params.remove_patch_regions ? "--remove_patch_regions" : ""
+
+    source = file_meta.source
+    synonym_file = genome_meta.synonym_file
+    rename_clinvar_ids = params.rename_clinvar_ids ? "--rename_clinvar_ids" : ""
+    sources = file_meta.sources
+    sources_meta_file = params.sources_meta_file
+
+    """
+    temp_file="removed_variants.vcf"
+    chrs=\$(tabix ${vcf} -l | xargs | tr ' ' ',')
+
+    update_fields.py \
+        ${vcf} \
+        ${source} \
+        ${synonym_file} \
+        ${rename_clinvar_ids} \
+        -O \${temp_file} \
+        --chromosomes \${chrs} \
+        --sources ${sources} \
+        --sources_meta_file ${sources_meta_file}
+
+    remove_variants.py \
+        \${temp_file} \
+        --chrom_sizes ${chrom_sizes} \
+        ${remove_nonunique_ids} \
+        ${remove_patch_regions} \
+        -O ${output_file}
+
+    bcftools index -f -c ${output_file}
+    """
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test
new file mode 100644
index 00000000..95ab4606
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test
@@ -0,0 +1,373 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process FORMAT_VCF"
+    script "../main.nf"
+    process "FORMAT_VCF"
+
+    test("remove criteria - all") {
+
+        when {
+            params {
+                remove_nonunique_ids = 1
+                remove_patch_regions = 1
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'dbSNP',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 13
+            assert lines[0].equals('##fileformat=VCFv4.4')
+            assert lines[1].equals('##FILTER=<ID=PASS,Description="All filters passed">')
+            assert lines[2].equals('##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of the variation data">')
+            assert lines[3].equals('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">')
+            assert lines[4].equals('##INFO=<ID=SVLEN,Number=.,Type=String,Description="Difference in length between REF and ALT alleles">')
+            assert lines[5].equals('##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">')
+            assert lines[6].equals('##contig=<ID=1>')
+            assert lines[7].equals('##contig=<ID=CHR_HSCHR1_3_CTG31>')
+            assert lines[8].equals('##contig=<ID=Y>')
+            assert lines[9].equals('##source="dbSNP" description="NCBI db of human variants" url="https://www.ncbi.nlm.nih.gov/snp/" version="157" accession_url="https://www.ncbi.nlm.nih.gov/snp/"')
+            assert lines[10].equals('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO')
+            assert lines[11].equals('1\t925952\t1019397\tG\tA\t.\t.\tSOURCE=dbSNP')
+            assert lines[12].equals('Y\t2787033\t652674\tAG\tA\t.\t.\tSOURCE=dbSNP')
+        }
+    }
+
+    test("remove criteria - non-unique ids") {
+
+        when {
+            params {
+                remove_nonunique_ids = 1
+                remove_patch_regions = 0
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'dbSNP',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 14
+            assert lines[0].equals('##fileformat=VCFv4.4')
+            assert lines[1].equals('##FILTER=<ID=PASS,Description="All filters passed">')
+            assert lines[2].equals('##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of the variation data">')
+            assert lines[3].equals('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">')
+            assert lines[4].equals('##INFO=<ID=SVLEN,Number=.,Type=String,Description="Difference in length between REF and ALT alleles">')
+            assert lines[5].equals('##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">')
+            assert lines[6].equals('##contig=<ID=1>')
+            assert lines[7].equals('##contig=<ID=CHR_HSCHR1_3_CTG31>')
+            assert lines[8].equals('##contig=<ID=Y>')
+            assert lines[9].equals('##source="dbSNP" description="NCBI db of human variants" url="https://www.ncbi.nlm.nih.gov/snp/" version="157" accession_url="https://www.ncbi.nlm.nih.gov/snp/"')
+            assert lines[10].equals('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO')
+            assert lines[11].equals('1\t925952\t1019397\tG\tA\t.\t.\tSOURCE=dbSNP')
+            assert lines[12].equals('CHR_HSCHR1_3_CTG31\t42\trs1656322366\tT\tG\t.\t.\tSOURCE=dbSNP')
+            assert lines[13].equals('Y\t2787033\t652674\tAG\tA\t.\t.\tSOURCE=dbSNP')
+        }
+    }
+
+    test("remove criteria - patch regions") {
+
+        when {
+            params {
+                remove_nonunique_ids = 0
+                remove_patch_regions = 1
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'dbSNP',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 14
+            assert lines[0].equals('##fileformat=VCFv4.4')
+            assert lines[1].equals('##FILTER=<ID=PASS,Description="All filters passed">')
+            assert lines[2].equals('##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of the variation data">')
+            assert lines[3].equals('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">')
+            assert lines[4].equals('##INFO=<ID=SVLEN,Number=.,Type=String,Description="Difference in length between REF and ALT alleles">')
+            assert lines[5].equals('##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">')
+            assert lines[6].equals('##contig=<ID=1>')
+            assert lines[7].equals('##contig=<ID=CHR_HSCHR1_3_CTG31>')
+            assert lines[8].equals('##contig=<ID=Y>')
+            assert lines[9].equals('##source="dbSNP" description="NCBI db of human variants" url="https://www.ncbi.nlm.nih.gov/snp/" version="157" accession_url="https://www.ncbi.nlm.nih.gov/snp/"')
+            assert lines[10].equals('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO')
+            assert lines[11].equals('1\t925952\t1019397\tG\tA\t.\t.\tSOURCE=dbSNP')
+            assert lines[12].equals('1\t198725174\trs1438337621\tT\tC,G\t.\t.\tSOURCE=dbSNP')
+            assert lines[13].equals('Y\t2787033\t652674\tAG\tA\t.\t.\tSOURCE=dbSNP')
+        }
+    }
+
+    test("remove criteria - none") {
+
+        when {
+            params {
+                remove_nonunique_ids = 0
+                remove_patch_regions = 0
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'dbSNP',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_format_vcf.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 16
+            assert lines[0].equals('##fileformat=VCFv4.4')
+            assert lines[1].equals('##FILTER=<ID=PASS,Description="All filters passed">')
+            assert lines[2].equals('##INFO=<ID=SOURCE,Number=1,Type=String,Description="Source of the variation data">')
+            assert lines[3].equals('##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">')
+            assert lines[4].equals('##INFO=<ID=SVLEN,Number=.,Type=String,Description="Difference in length between REF and ALT alleles">')
+            assert lines[5].equals('##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">')
+            assert lines[6].equals('##contig=<ID=1>')
+            assert lines[7].equals('##contig=<ID=CHR_HSCHR1_3_CTG31>')
+            assert lines[8].equals('##contig=<ID=Y>')
+            assert lines[9].equals('##source="dbSNP" description="NCBI db of human variants" url="https://www.ncbi.nlm.nih.gov/snp/" version="157" accession_url="https://www.ncbi.nlm.nih.gov/snp/"')
+            assert lines[10].equals('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO')
+            assert lines[11].equals('1\t925952\t1019397\tG\tA\t.\t.\tSOURCE=dbSNP')
+            assert lines[12].equals('1\t198725174\trs1438337621\tT\tC,G\t.\t.\tSOURCE=dbSNP')
+            assert lines[13].equals('CHR_HSCHR1_3_CTG31\t42\trs1656322366\tT\tG\t.\t.\tSOURCE=dbSNP')
+            assert lines[14].equals('CHR_HSCHR1_3_CTG31\t366579\trs1438337621\tT\tC,G\t.\t.\tSOURCE=dbSNP')
+            assert lines[15].equals('Y\t2787033\t652674\tAG\tA\t.\t.\tSOURCE=dbSNP')
+        }
+    }
+
+    test("multiple source") {
+
+        when {
+            params {
+                remove_nonunique_ids = 0
+                remove_patch_regions = 0
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'MULTIPLE',
+                        'sources':'CerealsDB,Watkins-exome-capture',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_multiple_source.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_multiple_source.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 12
+            assert lines[7].equals('##source="CerealsDB" description="Markers from Axiom 820K and 35K SNP Array  provided by <a href=\'http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php\'>CerealsDB<a/>n"')
+            assert lines[8].equals('##source="Watkins-exome-capture" description="103 accessions of the Watkins landrace collection"')
+            assert lines[10].equals('1A\t539\t1A_539\tACGGGA\tGCGGGA,GCGGAG\t.\t.\tSOURCE=Watkins-exome-capture')
+            assert lines[11].equals('1A\t1145499\tBA00441553\tC\tT\t.\t.\tSOURCE=CerealsDB')
+        }
+    }
+
+    test("SV fields - SVLEN and END") {
+
+        when {
+            params {
+                remove_nonunique_ids = 0
+                remove_patch_regions = 0
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'dbVar',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_structural_variant.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_structural_variant.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 11
+            assert lines[8].equals('1\t46000\tnsv4514092\tT\t<CNV>\t.\t.\tSOURCE=dbVar;END=111250')
+            assert lines[9].equals('1\t54665\tnsv4536437\tA\t<INS>\t.\t.\tSOURCE=dbVar;SVLEN=.')
+            assert lines[10].equals('1\t62399\tnsv4036772\tT\t<DEL>\t.\t.\tSOURCE=dbVar;SVLEN=-90;END=62489')
+        }
+    }
+
+    test("HGSVC field - NODEID") {
+
+        when {
+            params {
+                remove_nonunique_ids = 0
+                remove_patch_regions = 0
+            }
+            process {
+                """
+                genome_meta = [
+                        'synonym_file':"${projectDir}/tests/testdata/homo_sapiens_grch38.synonyms"
+                    ]
+                file_meta = [
+                        'source':'HGSVC3',
+                        'sources_meta_file':"${projectDir}/assets/sources_meta.json"
+                    ]
+                vcf = "${moduleTestDir}/testdata/test_hgsvc_variant.vcf.gz"
+                vcf_index = "${moduleTestDir}/testdata/test_hgsvc_variant.vcf.gz.tbi"
+
+                input[0] = tuple(
+                        genome_meta, 
+                        file_meta,
+                        file(vcf),
+                        file(vcf_index)
+                    )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // following is duplicate of snapshot match but for readability purpose
+            // should be used to check if snapshot is invalid
+            def lines = path(process.out.get(0).get(0).get(2)).linesGzip[0..-1]
+            assert lines.size() == 12
+            assert lines[5].equals('##INFO=<ID=NODEID,Number=1,Type=String,Description="Identifier of the nodes this variant belong to">')
+            assert lines[7].equals('##source="HGSVC3" description="The Human Genome Structural Variation Consortium (HGSVC, Phase 3) focus on developing resources and computational approaches to fully characterize and integrate structural variants into their haplotypic context in order to understand their mutational mechanisms and functional consequences" url="https://www.hgsvc.org/about" version="2025-03-01"')
+            assert lines[9].equals('1\t15938\t1:15938::\tC\tT\t.\t.\tSOURCE=HGSVC3;NODEID=>50021761>50021764')
+            assert lines[10].equals('1\t15967\t1:15967::5\tG\tCTGCCC\t.\t.\tSOURCE=HGSVC3;NODEID=>50021764>50021767')
+            assert lines[11].equals('1\t16182\t1:16182:12:\ttaTCAGCCTGGTa\tt\t.\t.\tSOURCE=HGSVC3;NODEID=>50021779>50021781')
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test.snap
new file mode 100644
index 00000000..c537eb0a
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/format_vcf/tests/main.nf.test.snap
@@ -0,0 +1,171 @@
+{
+    "multiple source": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "MULTIPLE",
+                            "sources": "CerealsDB,Watkins-exome-capture",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_multiple_source.vcf.vcf.gz:md5,d6b39975b118ff024dab0ce1fc04a992",
+                        "FORMATTED-null-test_multiple_source.vcf.vcf.gz.csi:md5,6567ac6c2a02c024bb21842e136358d6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:39:57.619654"
+    },
+    "remove criteria - none": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "dbSNP",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz:md5,ab2b6cd7de2c7193c4597db7b6a6c156",
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz.csi:md5,7fd004a9dc44474719245af94bef0c3a"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:39:53.643092"
+    },
+    "HGSVC field - NODEID": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "HGSVC3",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_hgsvc_variant.vcf.vcf.gz:md5,994f7153ef154e45d93af6b4e8e06106",
+                        "FORMATTED-null-test_hgsvc_variant.vcf.vcf.gz.csi:md5,be4839a47f476253b129a373f2d29dbe"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:40:05.468229"
+    },
+    "remove criteria - patch regions": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "dbSNP",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz:md5,e5454063e398e4514dea8ceffc7624ea",
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz.csi:md5,e3679835e0b3b67bd24e22666693385d"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:39:49.724133"
+    },
+    "SV fields - SVLEN and END": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "dbVar",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_structural_variant.vcf.vcf.gz:md5,142aa8e8158090e72d8f262a9b4bd6fe",
+                        "FORMATTED-null-test_structural_variant.vcf.vcf.gz.csi:md5,478352a43d80b1977fa48a3153e83cd3"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:40:01.486704"
+    },
+    "remove criteria - non-unique ids": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "dbSNP",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz:md5,63b3e60ffb6b468e4d05b816d98c507e",
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz.csi:md5,c575f44acc057dab03569206216469bc"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:39:45.750831"
+    },
+    "remove criteria - all": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950"
+                        },
+                        {
+                            "source": "dbSNP",
+                            "sources_meta_file": "sources_meta.json:md5,007a554fd8d0e9bce7cc7b3c0c62bbe5"
+                        },
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz:md5,95f9d4a073936c159a6e903f0b420d73",
+                        "FORMATTED-null-test_format_vcf.vcf.vcf.gz.csi:md5,d785d67afd1a83b4be340f5e88a8cb0d"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-16T12:39:41.960057"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz
new file mode 100644
index 00000000..74d09dba
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz.tbi
new file mode 100644
index 00000000..4976a595
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_format_vcf.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz
new file mode 100644
index 00000000..3faf2616
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz.tbi
new file mode 100644
index 00000000..ec53251d
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_hgsvc_variant.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz
new file mode 100644
index 00000000..65354267
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz.tbi
new file mode 100644
index 00000000..1f07e78e
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_multiple_source.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz
new file mode 100644
index 00000000..8fd50c10
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz.tbi
new file mode 100644
index 00000000..0b6c1997
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/format_vcf/tests/testdata/test_structural_variant.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/generate_chrom_sizes.nf b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/main.nf
similarity index 58%
rename from nextflow/vcf_prepper/modules/local/generate_chrom_sizes.nf
rename to nextflow/vcf_prepper/modules/local/generate_chrom_sizes/main.nf
index 1a3c4405..ae616210 100755
--- a/nextflow/vcf_prepper/modules/local/generate_chrom_sizes.nf
+++ b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/main.nf
@@ -15,33 +15,30 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process GENERATE_CHROM_SIZES {
-  label 'process_low'
-  cache false
-  
-  input:
-  val meta
+    label 'process_low'
+    cache false
+
+    input:
+    val genome_meta
+    val version
+    val ini_file
+
+    output:
+    tuple val(genome_meta), val(chrom_sizes_file)
+
+    script:
+    species = genome_meta.species
+    assembly = genome_meta.assembly
+    chrom_sizes_file = genome_meta.chrom_sizes_file
 
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  species = meta.species
-  assembly = meta.assembly
-  version = params.version
-  ini_file = params.ini_file
-  chrom_sizes = meta.chrom_sizes
-  force_create_config = params.force_create_config ? "--force" : ""
-  
-  '''
-  generate_chrom_sizes.py \
-    !{species} \
-    !{assembly} \
-    !{version} \
-    --ini_file !{ini_file} \
-    --chrom_sizes !{chrom_sizes} \
-    !{force_create_config}
-  '''
+    """
+    generate_chrom_sizes.py \
+        ${species} \
+        ${assembly} \
+        ${version} \
+        --ini_file ${ini_file} \
+        --chrom_sizes ${chrom_sizes_file}
+    """
 }
diff --git a/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test
new file mode 100644
index 00000000..d91eb018
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test
@@ -0,0 +1,56 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process GENERATE_CHROM_SIZES"
+    script "../main.nf"
+    process "GENERATE_CHROM_SIZES"
+
+    test("chrom_sizes") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    'genome':'homo_sapiens_grch38', 
+                    'species':'homo_sapiens', 
+                    'assembly':'GRCh38',
+                    'chrom_sizes_file':"${workDir}/homo_sapiens_grch38.chrom.sizes"
+                ]
+                input[1] = 110
+                input[2] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // genome_meta should be same as input
+            assert process.out.get(0).get(0).get(0) == [
+                    'genome':'homo_sapiens_grch38', 
+                    'species':'homo_sapiens', 
+                    'assembly':'GRCh38',
+                    'chrom_sizes_file':"${workDir}/homo_sapiens_grch38.chrom.sizes"
+                ]
+            assert path("${workDir}/homo_sapiens_grch38.chrom.sizes").md5 == "77e059be395da32b566fe37a13439427"
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test.snap
new file mode 100644
index 00000000..643424c4
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/generate_chrom_sizes/tests/main.nf.test.snap
@@ -0,0 +1,24 @@
+{
+    "chrom_sizes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome": "homo_sapiens_grch38",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38",
+                            "chrom_sizes_file": "homo_sapiens_grch38.chrom.sizes:md5,77e059be395da32b566fe37a13439427"
+                        },
+                        "homo_sapiens_grch38.chrom.sizes:md5,77e059be395da32b566fe37a13439427"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-07T17:12:35.866894"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/generate_synonym_file.nf b/nextflow/vcf_prepper/modules/local/generate_synonym_file/main.nf
similarity index 58%
rename from nextflow/vcf_prepper/modules/local/generate_synonym_file.nf
rename to nextflow/vcf_prepper/modules/local/generate_synonym_file/main.nf
index 876f2861..d5c6ddae 100755
--- a/nextflow/vcf_prepper/modules/local/generate_synonym_file.nf
+++ b/nextflow/vcf_prepper/modules/local/generate_synonym_file/main.nf
@@ -15,33 +15,30 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process GENERATE_SYNONYM_FILE {
-  label 'process_low'
-  cache false
-  
-  input:
-  val meta
-  
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  species = meta.species
-  assembly = meta.assembly
-  version = params.version
-  ini_file = params.ini_file
-  synonym_file = meta.synonym_file
-  force_create_config = params.force_create_config ? "--force" : ""
-  
-  '''
-  generate_synonym_file.py \
-    !{species} \
-    !{assembly} \
-    !{version} \
-    --ini_file !{ini_file} \
-    --synonym_file !{synonym_file} \
-    !{force_create_config}
-  '''
+    label 'process_low'
+    cache false
+
+    input:
+    val genome_meta
+    val version
+    val ini_file
+
+    output:
+    tuple val(genome_meta), val(synonym_file)
+
+    script:
+    species = genome_meta.species
+    assembly = genome_meta.assembly
+    synonym_file = genome_meta.synonym_file
+
+    """
+    generate_synonym_file.py \
+        ${species} \
+        ${assembly} \
+        ${version} \
+        --ini_file ${ini_file} \
+        --synonym_file ${synonym_file}
+    """
 }
diff --git a/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test
new file mode 100644
index 00000000..92d0e282
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test
@@ -0,0 +1,57 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process GENERATE_SYNONYM_FILE"
+    script "../main.nf"
+    process "GENERATE_SYNONYM_FILE"
+
+    test("synonym_file") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    'genome':'homo_sapiens_grch38', 
+                    'species':'homo_sapiens', 
+                    'assembly':'GRCh38',
+                    'synonym_file':"${workDir}/homo_sapiens_grch38.synonyms"
+                ]
+                input[1] = 110
+                input[2] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // genome_meta should be same as input
+            assert process.out.get(0).get(0).get(0) == [
+                    'genome':'homo_sapiens_grch38', 
+                    'species':'homo_sapiens', 
+                    'assembly':'GRCh38',
+                    'synonym_file':"${workDir}/homo_sapiens_grch38.synonyms"
+                ]
+            assert path("${workDir}/homo_sapiens_grch38.synonyms").md5 == "2e6bf0348c272e8d6c9829e4cb50d585"
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test.snap
new file mode 100644
index 00000000..d3d84819
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/generate_synonym_file/tests/main.nf.test.snap
@@ -0,0 +1,24 @@
+{
+    "synonym_file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome": "homo_sapiens_grch38",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38",
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,2e6bf0348c272e8d6c9829e4cb50d585"
+                        },
+                        "homo_sapiens_grch38.synonyms:md5,2e6bf0348c272e8d6c9829e4cb50d585"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-07T16:09:18.082914"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/generate_tracks_perl.nf b/nextflow/vcf_prepper/modules/local/generate_tracks_perl.nf
deleted file mode 100755
index 2240e883..00000000
--- a/nextflow/vcf_prepper/modules/local/generate_tracks_perl.nf
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process GENERATE_TRACKS_PERL {
-  input: 
-  tuple val(source), val(vcfFile)
-  
-  shell:
-  '''
-  vcf_file="!{vcfFile}"
-  source="!{source}"
-  
-  # remove any whitespace in source name
-  source=${source// /_}
-  
-  # if vcf file is uncompressed we need to compress it
-  temp_dir=${PWD}/${source}_temp
-  mkdir -p ${temp_dir}  
-  file_type=$(file ${vcf_file})
-  if [[ ! ${file_type} =~ compressed ]]; then
-    # compress vcf file
-    vcf_filename=$(basename ${vcf_file})
-    compressed_vcf=${temp_dir}/${vcf_filename/.gz/}
-    bgzip -c ${vcf_file} > ${compressed_vcf}
-    
-    # set the vcf_file to compressed vcf file
-    vcf_file=${compressed_vcf}
-  fi
-  
-  # tabix index the compressed vcf file if not already exist
-  tabix ${vcf_file} -l > /dev/null 2>&1 || tabix -p vcf -f ${vcf_file}
-  
-  out_dir=${PWD}/${source}_out
-  mkdir -p ${out_dir}
-  
-  config_dir=!{projectDir}/assets
-  
-  # run the track generation script
-  generate_tracks.pl ${vcf_file} ${out_dir} ${config_dir}
-
-  # remove temp dir with compressed vcf file
-  if [[ -d ${temp_dir} ]]; then
-    rm -r ${temp_dir}
-  fi
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/generate_vep_config.nf b/nextflow/vcf_prepper/modules/local/generate_vep_config.nf
deleted file mode 100755
index 33c81a37..00000000
--- a/nextflow/vcf_prepper/modules/local/generate_vep_config.nf
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process GENERATE_VEP_CONFIG {
-  cache false
-  
-  input:
-  val meta
-    
-  output:
-  val genome
-  
-  shell:
-  force_create_config = params.force_create_config
-  genome = meta.genome
-  version = params.version
-  species = meta.species
-  assembly = meta.assembly
-  genome_uuid = meta.genome_uuid
-  ini_file = params.ini_file
-  vep_config = meta.vep_config
-  fasta_dir = meta.fasta_dir
-  cache_dir = params.use_vep_cache ? "--cache_dir ${meta.cache_dir}" : ""
-  gff_dir = params.use_vep_cache ? "" : "--gff_dir ${meta.gff_dir}"
-  conservation_data_dir = meta.conservation_data_dir
-  repo_dir = params.repo_dir
-  structural_variant = params.structural_variant ? "--structural_variant" : ""
-
-  if (params.population_data_file) {
-    population_data_file = "--population_data_file " + params.population_data_file
-  }
-  else if (!params.structural_variant && file("${projectDir}/assets/population_data.json").exists()){
-    population_data_file = "--population_data_file " + "${projectDir}/assets/population_data.json"
-  }
-  else {
-    population_data_file = ""
-  }
-  use_old_infra = params.use_old_infra ? "--use_old_infra" : ""
-  
-  '''
-  if [[ ! -e !{vep_config} || !{force_create_config} == 1 ]]; then
-    generate_vep_config.py \
-      !{version} \
-      !{species} \
-      !{assembly} \
-      --genome_uuid !{genome_uuid} \
-      --ini_file !{ini_file} \
-      --vep_config !{vep_config} \
-      --fasta_dir !{fasta_dir} \
-      !{cache_dir} \
-      !{gff_dir} \
-      --conservation_data_dir !{conservation_data_dir} \
-      --repo_dir !{repo_dir} \
-      !{population_data_file} \
-      !{structural_variant} \
-      !{use_old_infra}
-  fi
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/index_vcf.nf b/nextflow/vcf_prepper/modules/local/index_vcf.nf
deleted file mode 100755
index dfb1a891..00000000
--- a/nextflow/vcf_prepper/modules/local/index_vcf.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process INDEX_VCF {
-  label 'bcftools'
-  
-  input:
-  tuple val(meta), path(vcf)
-  
-  output:
-  tuple val(meta), path(new_vcf), path(vcf_index)
-  
-  shell:
-  index_type = meta.index_type
-  flag_index = (index_type == "tbi" ? "-t" : "-c")
-  new_vcf = "${meta.genome}-${meta.source}.vcf.gz"
-  vcf_index = new_vcf + ".${index_type}"
-  
-  '''
-  ln -sf !{vcf} !{new_vcf}
-  bcftools index !{flag_index} !{new_vcf}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/process_cache.nf b/nextflow/vcf_prepper/modules/local/process_cache.nf
deleted file mode 100755
index 52fa89ff..00000000
--- a/nextflow/vcf_prepper/modules/local/process_cache.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process PROCESS_CACHE {
-  cache false
-  
-  input:
-  val meta
-
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  species = meta.species
-  assembly = meta.assembly
-  version = params.version
-  ini_file = params.ini_file
-  cache_dir = meta.cache_dir
-  force_create_config = params.force_create_config ? "--force" : ""
-  
-  '''
-  process_cache.py \
-    !{species} \
-    !{assembly} \
-    !{version} \
-    --ini_file !{ini_file} \
-    --cache_dir !{cache_dir} \
-    !{force_create_config}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/process_conservation_data.nf b/nextflow/vcf_prepper/modules/local/process_conservation_data.nf
deleted file mode 100755
index 55e2c669..00000000
--- a/nextflow/vcf_prepper/modules/local/process_conservation_data.nf
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process PROCESS_CONSERVATION_DATA {
-  cache false
-  
-  input:
-  val meta
-
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  species = meta.species
-  assembly = meta.assembly
-  version = params.version
-  ini_file = params.ini_file
-  conservation_data_dir = meta.conservation_data_dir
-  force_create_config = params.force_create_config ? "--force" : ""
-  
-  '''
-  process_conservation_data.py \
-    !{species} \
-    !{assembly} \
-    !{version} \
-    --ini_file !{ini_file} \
-    --conservation_data_dir !{conservation_data_dir} \
-    !{force_create_config}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/process_fasta.nf b/nextflow/vcf_prepper/modules/local/process_fasta.nf
deleted file mode 100755
index 4ac7153d..00000000
--- a/nextflow/vcf_prepper/modules/local/process_fasta.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process PROCESS_FASTA {
-  label 'process_medium'
-  cache false
-  
-  input:
-  val meta
-
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  species = meta.species
-  genome_uuid = meta.genome_uuid
-  assembly = meta.assembly
-  version = params.version
-  out_dir = meta.genome_temp_dir
-  ini_file = params.ini_file
-  fasta_dir = meta.fasta_dir
-  force_create_config = params.force_create_config ? "--force" : ""
-  use_old_infra = params.use_old_infra ? "--use_old_infra" : ""
-  
-  '''
-  process_fasta.py \
-    --species !{species} \
-    --genome_uuid !{genome_uuid} \
-    --assembly !{assembly} \
-    --version !{version} \
-    --out_dir !{out_dir} \
-    --ini_file !{ini_file} \
-    --fasta_dir !{fasta_dir} \
-    !{force_create_config} \
-    !{use_old_infra}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/process_gff.nf b/nextflow/vcf_prepper/modules/local/process_gff.nf
deleted file mode 100755
index fdc607bd..00000000
--- a/nextflow/vcf_prepper/modules/local/process_gff.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-
-process PROCESS_GFF {
-  cache false
-  
-  input:
-  val meta
-
-  output:
-  val genome
-  
-  shell:
-  genome = meta.genome
-  genome_uuid = meta.genome_uuid
-  release_id = meta.release_id
-  version = params.version
-  out_dir = meta.genome_temp_dir
-  ini_file = params.ini_file
-  gff_dir = meta.gff_dir
-  force_create_config = params.force_create_config ? "--force" : ""
-  
-  '''
-  process_gff.py \
-    !{genome_uuid} \
-    !{release_id} \
-    --out_dir !{out_dir} \
-    --ini_file !{ini_file} \
-    --gff_dir !{gff_dir} \
-    !{force_create_config}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/process_input.nf b/nextflow/vcf_prepper/modules/local/process_input.nf
deleted file mode 100755
index c4326d6a..00000000
--- a/nextflow/vcf_prepper/modules/local/process_input.nf
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-import java.net.*
-import java.io.*
-
-def remote_exists(url){
-    try {
-      HttpURLConnection.setFollowRedirects(false);
-      HttpURLConnection connection =
-         (HttpURLConnection) new URL(url).openConnection();
-      connection.setRequestMethod("HEAD");
-      return (connection.getResponseCode() == HttpURLConnection.HTTP_OK);
-    }
-    catch (Exception e) {
-       e.printStackTrace();
-       return false;
-    }
-}
-
-process PROCESS_INPUT {
-  cache false
-  errorStrategy 'retry'
-  maxRetries 3
-  
-  input:
-  tuple val(meta), val(vcf)
-
-  output:
-  tuple val(meta), val(output_vcf), val("${output_vcf}.${index_type}")
-  
-  shell:
-  file_type = meta.file_type
-  output_vcf = file_type == "remote" ? meta.genome_temp_dir + "/" + file(vcf).getName() : vcf
-  if(file_type == "remote") {
-    index_type = remote_exists(vcf + ".tbi") ? "tbi" : "csi"
-  }
-  else {
-    index_type = file(vcf + ".tbi").exists() ? "tbi" : "csi"
-  }
-  meta.index_type = index_type
-  
-  '''
-  if [[ !{file_type} == "remote" ]]; then
-    wget !{vcf} -O !{output_vcf}
-    wget !{vcf}.!{index_type} -O !{output_vcf}.!{index_type}
-  fi
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/read_vcf_chr.nf b/nextflow/vcf_prepper/modules/local/read_vcf_chr/main.nf
similarity index 68%
rename from nextflow/vcf_prepper/modules/local/read_vcf_chr.nf
rename to nextflow/vcf_prepper/modules/local/read_vcf_chr/main.nf
index f3113034..28f1b388 100755
--- a/nextflow/vcf_prepper/modules/local/read_vcf_chr.nf
+++ b/nextflow/vcf_prepper/modules/local/read_vcf_chr/main.nf
@@ -15,16 +15,23 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process READ_VCF_CHR {
-  input:
-  tuple val(meta), path(vcf), path(vcf_index)
+    input:
+    tuple val(genome_meta), 
+		val(file_meta),
+		path(vcf), 
+		path(vcf_index)
 
-  output:
-  tuple val(meta), path(vcf), path(vcf_index), path("*.chrom")
+    output:
+    tuple val(genome_meta), 
+		val(file_meta),
+		path(vcf), 
+		path(vcf_index), 
+		path("*.chrom")
 
-  shell:
-  '''
-  tabix !{vcf} -l | awk '{print $1".chrom"}' | xargs touch
-  '''
+    script:
+    """
+    tabix ${vcf} -l | awk '{print \$1".chrom"}' | xargs touch
+    """
 }
diff --git a/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test
new file mode 100644
index 00000000..7dc7e71e
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test
@@ -0,0 +1,44 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process READ_VCF_CHR"
+    script "../main.nf"
+    process "READ_VCF_CHR"
+
+	test("read_vcf_chr") {
+
+        when {
+            process {
+                """                
+                vcf = file("${moduleDir}/tests/testdata/test.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf.gz.csi")
+
+                input[0] = tuple([:], [:], vcf, vcf_index)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            assert file(process.out.get(0).get(0).get(4)).name == "1.chrom"
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test.snap
new file mode 100644
index 00000000..6c86607e
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "read_vcf_chr": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            
+                        },
+                        "test.vcf.gz:md5,44d9d1ba5029c6cba0dec462b51c896e",
+                        "test.vcf.gz.csi:md5,a6301281821ce62556b49e3e2bec061b",
+                        "1.chrom:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-03T10:33:32.327815"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz
new file mode 100755
index 00000000..565bfca6
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..48392c5e
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/read_vcf_chr/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/modules/local/remove_variants.nf b/nextflow/vcf_prepper/modules/local/remove_variants.nf
deleted file mode 100755
index 39f0b34d..00000000
--- a/nextflow/vcf_prepper/modules/local/remove_variants.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process REMOVE_VARIANTS {
-  input:
-  tuple val(meta), path(vcf)
-  
-  output:
-  tuple val(meta), path(output_file)
-
-  memory { (vcf.size() * 16.B + 2.GB) * task.attempt }
-  
-  shell:
-  output_file =  "REMOVED_" + file(vcf).getName()
-  chrom_sizes = meta.chrom_sizes
-  remove_nonunique_ids = params.remove_nonunique_ids ? "--remove_nonunique_ids" : ""
-  remove_patch_regions = params.remove_patch_regions ? "--remove_patch_regions" : ""
-  
-  '''
-  pyenv local variation-eva
-  remove_variants.py \
-    !{vcf} \
-    --chrom_sizes !{chrom_sizes} \
-    !{remove_nonunique_ids} \
-    !{remove_patch_regions} \
-    -O !{output_file}
-  '''
-}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/split_vcf_chr.nf b/nextflow/vcf_prepper/modules/local/split_vcf_chr/main.nf
similarity index 60%
rename from nextflow/vcf_prepper/modules/local/split_vcf_chr.nf
rename to nextflow/vcf_prepper/modules/local/split_vcf_chr/main.nf
index e1ecb3df..aeeceb56 100755
--- a/nextflow/vcf_prepper/modules/local/split_vcf_chr.nf
+++ b/nextflow/vcf_prepper/modules/local/split_vcf_chr/main.nf
@@ -17,24 +17,27 @@
  */
  
 process SPLIT_VCF_CHR {
-  label 'bcftools'
-  
-  input:
-  tuple val(meta), path(vcf), path(index_file), path(chr_file)
+    label 'bcftools'
 
-  output:
-  tuple val(meta), path("split.*.vcf.gz")
+    memory { 32.GB * task.attempt }
 
-  memory { 32.GB * task.attempt }
+    input:
+    tuple val(genome_meta), 
+		val(file_meta),
+		path(vcf), 
+		path(index_file), 
+		path(chr_file)
 
-  shell:
-  
-  '''
-  chr_file=!{chr_file}
-  chr=$(basename ${chr_file/.chrom/})
-  
-  bcftools view -Oz -o split.${chr}.vcf.gz !{vcf} "${chr}"
-  
-  rm ${chr_file}
-  '''
+    output:
+    tuple val(genome_meta), val(file_meta), path("split.*.vcf.gz")
+
+    script:
+    """
+    chr_file=${chr_file}
+    chr=\$(basename \${chr_file/.chrom/})
+    
+    bcftools view -Oz -o split.\${chr}.vcf.gz ${vcf} "\${chr}"
+    
+    rm ${chr_file}
+    """
 }
diff --git a/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test
new file mode 100644
index 00000000..866a7473
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test
@@ -0,0 +1,46 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process SPLIT_VCF_CHR"
+    script "../main.nf"
+    process "SPLIT_VCF_CHR"
+
+	test("split_vcf_chr") {
+
+        when {
+            process {
+                """                
+                vcf = file("${moduleDir}/tests/testdata/test.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf.gz.csi")
+				chr_file = "1.chrom"
+				file(chr_file).mkdirs()
+
+                input[0] = tuple([:], [:], vcf, vcf_index, file(chr_file))
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            assert file(process.out.get(0).get(0).get(2)).name == "split.1.vcf.gz"
+            assert path(process.out.get(0).get(0).get(2)).vcf.chromosomes == ['1'] as Set
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test.snap
new file mode 100644
index 00000000..ca2a4956
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "split_vcf_chr": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        "split.1.vcf.gz:md5,a19372541b6b26a1fd320ff098101d81"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-18T22:42:27.687606"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz
new file mode 100644
index 00000000..5f498d9a
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..e206e6b1
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/split_vcf_chr/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/modules/local/stage_file/main.nf b/nextflow/vcf_prepper/modules/local/stage_file/main.nf
new file mode 100644
index 00000000..2d438298
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/stage_file/main.nf
@@ -0,0 +1,72 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+def remote_exists(url){
+    try {
+        HttpURLConnection.setFollowRedirects(false);
+        HttpURLConnection connection =
+            new URL(url).openConnection();
+        connection.setRequestMethod("HEAD");
+        return (connection.getResponseCode() == HttpURLConnection.HTTP_OK);
+    }
+    catch (Exception e) {
+        e.printStackTrace();
+        return false;
+    }
+}
+
+process STAGE_FILE {
+    cache false
+    errorStrategy 'retry'
+    maxRetries 3
+
+    input:
+    tuple val(genome_meta), 
+        val(file_meta),
+        val(file)
+
+    output:
+    tuple val(genome_meta), 
+        val(file_meta),
+        path(output_file),
+        path("${output_file}.${index_type}")
+
+    script:
+    file_type = file_meta.file_type
+    output_file = file(file).getName()
+    // new Utils
+
+    if (file_type == "remote") {
+        index_type = remote_exists(file + ".tbi") ? "tbi" : "csi"
+    }
+    else {
+        index_type = file(file + ".tbi").exists() ? "tbi" : "csi"
+    }
+    file_meta.index_type = index_type
+
+    """
+    if [[ ${file_type} == "remote" ]]; then
+        wget ${file} -O ${output_file}
+        wget ${file}.${index_type} -O ${output_file}.${index_type}
+    else
+        ln -s ${file} ${output_file}
+        ln -s ${file}.${index_type} ${output_file}.${index_type}
+    fi
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test
new file mode 100644
index 00000000..077a76a3
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test
@@ -0,0 +1,87 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test Process STAGE_FILE"
+    script "../main.nf"
+    process "STAGE_FILE"
+
+    test('remote file - tbi index') {
+
+        when {
+            process {
+                """
+                genome_meta = [:]
+                file_meta = [:]
+                file_meta["file_type"] = "remote"
+                file = "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd14.GRCh38.variant_call.vcf.gz"
+
+                input[0] = tuple(genome_meta, file_meta, file)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test('remote file - csi index') {
+
+        when {
+            process {
+                """
+                genome_meta = [:]
+                file_meta = [:]
+                file_meta["file_type"] = "remote"
+                file = "https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_6/by_species/triticum_aestivum/GCA_900519105.1/4565_GCA_900519105.1_merged_ids.vcf.gz"
+
+                input[0] = tuple(genome_meta, file_meta, file)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+        test('local file') {
+
+        when {
+            process {
+                """
+                genome_meta = [:]
+                file_meta = [:]
+                file_meta["file_type"] = "local"
+                file = "${projectDir}/assets/examples/test.vcf.gz"
+
+                input[0] = tuple(genome_meta, file_meta, file)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test.snap
new file mode 100644
index 00000000..6727d1cb
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/stage_file/tests/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "remote file - csi index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            "file_type": "remote",
+                            "index_type": "csi"
+                        },
+                        "4565_GCA_900519105.1_merged_ids.vcf.gz:md5,cb6801a0d08fe4581f70aaac6000758d",
+                        "4565_GCA_900519105.1_merged_ids.vcf.gz.csi:md5,e3b2e0b612551a1e91aa62c10c44bed0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-01-29T17:02:58.634386"
+    },
+    "remote file - tbi index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            "file_type": "remote",
+                            "index_type": "tbi"
+                        },
+                        "nstd14.GRCh38.variant_call.vcf.gz:md5,82a35ce24dc0b01cce4560db78709346",
+                        "nstd14.GRCh38.variant_call.vcf.gz.tbi:md5,ada3c4753f2d8e3c6d8077d48b28e2bb"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-02-02T09:50:35.948501"
+    },
+    "local file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            "file_type": "local",
+                            "index_type": "tbi"
+                        },
+                        "test.vcf.gz:md5,560da8fb0e369a5f081612d16c4b782b",
+                        "test.vcf.gz.tbi:md5,d3315c425f3fcb918db7e685ea47adfd"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-01-29T17:03:02.185657"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats.nf b/nextflow/vcf_prepper/modules/local/summary_stats.nf
deleted file mode 100755
index 8c2041b9..00000000
--- a/nextflow/vcf_prepper/modules/local/summary_stats.nf
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process SUMMARY_STATS { 
-  input: 
-  tuple val(meta), path(vcf), path(vcf_index)
-
-  output:
-  tuple val(meta), path(output_file), path(vcf_index)
-
-  memory  { ((vcf.size() * 1.25 * 1.B) + 2.GB) * task.attempt }
-
-  shell:
-  species = meta.species
-  assembly = meta.assembly
-  output_file =  "UPDATED_SS_" + file(vcf).getName()
-  index_type = meta.index_type
-  flag_index = (index_type == "tbi" ? "-t" : "-c")
-  vcf_index = output_file + ".${index_type}"
-  
-  if (params.population_data_file) {
-    population_data_file = "--population_data_file " + params.population_data_file
-  }
-  else if (!params.structural_variant && file("${projectDir}/assets/population_data.json").exists()){
-    population_data_file = "--population_data_file " + "${projectDir}/assets/population_data.json"
-  }
-  else {
-    population_data_file = ""
-  }
-
-  '''
-  summary_stats.py \
-    !{species} \
-    !{assembly} \
-    !{vcf} \
-    -O !{output_file} \
-    !{population_data_file}
-  
-  bcftools index !{flag_index} !{output_file}
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats/main.nf b/nextflow/vcf_prepper/modules/local/summary_stats/main.nf
new file mode 100755
index 00000000..ed18a911
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/summary_stats/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process SUMMARY_STATS {
+	memory { ((vcf.size() * 1.25 * 1.B) + 2.GB) * task.attempt }
+
+	input:
+	tuple val(genome_meta), 
+		val(file_meta),
+		path(vcf), 
+		path(vcf_index)
+	val population_data_file
+
+	output:
+	tuple val(genome_meta), 
+		val(file_meta),
+		path(output_file), 
+		path(vcf_index)
+
+	script:
+	species = genome_meta.species
+	assembly = genome_meta.assembly
+	output_file = "POST_FORMATTED_" + file(vcf).getName()
+
+	index_type = "csi"
+	flag_index = (index_type == "tbi" ? "-t" : "-c")
+	vcf_index = output_file + ".${index_type}"
+
+	population_data_file_param = population_data_file != "NONE"
+		? "--population_data_file " + params.population_data_file
+		: ""
+
+	"""
+	summary_stats.py \
+		${species} \
+		${assembly} \
+		${vcf} \
+		-O ${output_file} \
+		${population_data_file_param}
+	
+	bcftools index ${flag_index} ${output_file}
+	"""
+}
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test
new file mode 100644
index 00000000..7081c14e
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test
@@ -0,0 +1,92 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process SUMMARY_STATS"
+    script "../main.nf"
+    process "SUMMARY_STATS"
+
+	test("summary_stats - population.json is 'NONE'") {
+
+        when {
+            process {
+                """                
+                genome_meta = [
+                        'species':'homo_sapiens',
+                        'assembly':'GRCh38'
+                    ]
+				file_meta = [:]
+                vcf = file("${moduleDir}/tests/testdata/test.vcf_VEP.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf_VEP.vcf.gz.csi")
+
+                input[0] = tuple(genome_meta, file_meta, vcf, vcf_index)
+				input[1] = "NONE"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+			assert snapshot(process.out).match()
+
+            def out_vcf = path(process.out.get(0).get(0).get(2)).vcf
+
+            // file content ok
+            assert out_vcf.variants.size() == 1
+            assert out_vcf.variantsMD5 == 'd02d526bfcb5ffeae9f836987211fd6a'
+
+            // header has summary stats tag
+            assert out_vcf.header.hasInfoLine('NTCSQ')
+            assert out_vcf.header.hasInfoLine('NRCSQ')
+            assert out_vcf.header.hasInfoLine('NGENE')
+            assert out_vcf.header.hasInfoLine('NVPHN')
+            assert out_vcf.header.hasInfoLine('NGPHN')
+            assert out_vcf.header.hasInfoLine('NCITE')
+            assert out_vcf.header.hasInfoLine('RAF')
+
+            // corrent summary stats value
+            assert out_vcf.getInfoTag('NTCSQ', "1", 230710048) == '12'
+            assert out_vcf.getInfoTag('NGENE', "1", 230710048) == '1'
+		}
+    }
+
+    test("summary_stats - no RAF") {
+
+        when {
+            process {
+                """                
+                genome_meta = [
+                        'species':'homo_sapiens',
+                        'assembly':'GRCh38'
+                    ]
+				file_meta = [:]
+                vcf = file("${moduleDir}/tests/testdata/test.vcf_VEP.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf_VEP.vcf.gz.csi")
+
+                input[0] = tuple(genome_meta, file_meta, vcf, vcf_index)
+				input[1] = "${projectDir}/assets/population_data.json"
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+			assert process.errorReport.contains("Unable to retrieve CSQ field index for RAF")
+		}
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test.snap
new file mode 100644
index 00000000..69d3d71c
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/summary_stats/tests/main.nf.test.snap
@@ -0,0 +1,26 @@
+{
+    "summary_stats - population.json is 'NONE'": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38"
+                        },
+                        {
+                            
+                        },
+                        "POST_FORMATTED_test.vcf_VEP.vcf.gz:md5,7080d9b08465c9fd09967a9a0ccb5ce1",
+                        "POST_FORMATTED_test.vcf_VEP.vcf.gz.csi:md5,ac41a6a02a0c5309d24c52d088221534"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-03T10:30:35.252148"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz b/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz
new file mode 100644
index 00000000..e6aed940
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz.tbi
new file mode 100644
index 00000000..d3c5e7b5
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/summary_stats/tests/testdata/test.vcf_VEP.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/update_fields.nf b/nextflow/vcf_prepper/modules/local/update_fields.nf
deleted file mode 100755
index 1ebb464c..00000000
--- a/nextflow/vcf_prepper/modules/local/update_fields.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-process UPDATE_FIELDS {
-  label 'process_medium'
-
-  input: 
-  tuple val(meta), path(vcf), path(vcf_index)
-  
-  output:
-  tuple val(meta), path(output_file)
-  
-  shell:
-  output_file = "UPDATED_S_" + file(vcf).getName()
-  source = meta.source
-  synonym_file = meta.synonym_file
-  rename_clinvar_ids = params.rename_clinvar_ids ? "--rename_clinvar_ids" : ""
-  sources = meta.sources
-  sources_meta_file = params.sources_meta_file
-
-  '''
-  chrs=$(tabix !{vcf} -l | xargs | tr ' ' ',')
-  update_fields.py !{vcf} !{source} !{synonym_file} \
-    !{rename_clinvar_ids} \
-    -O !{output_file} \
-    --chromosomes ${chrs} \
-    --sources !{sources} \
-    --sources_meta_file !{sources_meta_file}
-  '''
-}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed.nf b/nextflow/vcf_prepper/modules/local/vcf_to_bed/main.nf
similarity index 56%
rename from nextflow/vcf_prepper/modules/local/vcf_to_bed.nf
rename to nextflow/vcf_prepper/modules/local/vcf_to_bed/main.nf
index fa0aa4bd..a45a4a9f 100755
--- a/nextflow/vcf_prepper/modules/local/vcf_to_bed.nf
+++ b/nextflow/vcf_prepper/modules/local/vcf_to_bed/main.nf
@@ -15,22 +15,29 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 process VCF_TO_BED {
-  input: 
-  path rank_file
-  tuple val(meta), path(vcf) 
-  
-  output:
-  tuple val(meta), path(output_file)
-  
-  shell:
-  output_file = vcf.getName().replace(".vcf.gz", ".bed")
-  structural_variant = params.structural_variant
-  
-  '''
-  vcf_to_bed !{vcf} !{output_file} !{rank_file} !{structural_variant}
+    input:
+    tuple val(genome_meta), val(file_meta), path(vcf)
+    path rank_file
+    val bed_fields
+    val structural_variant
+
+    output:
+    tuple val(genome_meta), val(file_meta), path(output_file)
+
+    script:
+    output_file = vcf.getName().replace(".vcf.gz", ".bed")
+    structural_variant_param = structural_variant ? "--structural-variant" : ""
+
+    """
+    vcf_to_bed \
+        --vcf ${vcf} \
+        --output ${output_file} \
+        --rank ${rank_file} \
+        --bed-fields ${bed_fields} \
+        ${structural_variant_param}
     
-  rm !{vcf}
-  '''
+    rm ${vcf}
+    """
 }
diff --git a/nextflow/vcf_prepper/tests/modules/local/vcf_to_bed.nf.test b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test
old mode 100755
new mode 100644
similarity index 60%
rename from nextflow/vcf_prepper/tests/modules/local/vcf_to_bed.nf.test
rename to nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test
index a49e6c09..931f60c9
--- a/nextflow/vcf_prepper/tests/modules/local/vcf_to_bed.nf.test
+++ b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test
@@ -1,43 +1,50 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
 nextflow_process {
 
     name "Test Process VCF_TO_BED"
-    script "modules/local/vcf_to_bed.nf"
+    script "../main.nf"
     process "VCF_TO_BED"
 
-    test("Should run without failures") {
+    test("vcf_to_bed - short_variants") {
 
         when {
-            params {
-                rank_file = "${baseDir}/assets/variation_consequnce_rank.json"
-            }
             process {
                 """
-                input[0] = params.rank_file
-                input[1] = tuple("NONE", file("$baseDir/tests/data/test_vcftobed.vcf.gz"))
+                input[0] = tuple([:], [:], file("${moduleDir}/tests/testdata/test_vcftobed.vcf.gz"))
+                input[1] = "${projectDir}/assets/variation_consequnce_rank.json"
+                input[2] = "${projectDir}/assets/short_variant_bedfields.json"
+                input[3] = false
                 """
             }
         }
 
         then {
-            // assert process run correctly
-            assert process.success
-            
-            // assert each output items value
-            // here get(0) gives the first ouput channel - we can use the name if we have used emit
-            with (process.out.get(0)) {
-                // output is a tuple which gives unordered list of ordered list. So we have to delve with two nested loop
-                with (get(0)) {
-                  assert get(0) == "NONE"
-                  assert get(1) ==~ ".*/test_vcftobed.bed"
-                }
-            }  
+			// not checking snapshot - for multi-allelic the alleles can come in any order
+            assert process.success 
             
             // assert the content of the output file
-            def output_file = file(process.out.get(0).get(0).get(1))
+            def output_file = file(process.out.get(0).get(0).get(2))
             def lines = output_file.readLines()
             assert lines.size() == 14
             
             // vcf file line 2: ignored - rsID equals to "."
+			// so, no line in bed file
             
             // vcf file line 4: bi-allelic SNV
             assert lines[2] == "chr13 32357724 32357725 rs754065641 SNV G C 2 splice_polypyrimidine_tract_variant"
@@ -97,4 +104,48 @@ nextflow_process {
 
     }
 
+	test("vcf_to_bed - --structural_variant for symbolic alts") {
+
+        when {
+            process {
+                """
+                input[0] = tuple([:], [:], file("${moduleDir}/tests/testdata/test_symbolic.vcf.gz"))
+                input[1] = "${projectDir}/assets/variation_consequnce_rank.json"
+                input[2] = "${projectDir}/assets/structural_variant_bedfields.json"
+                input[3] = true
+                """
+            }
+        }
+
+		then {
+			assert process.success
+            assert snapshot(process.out).match()
+
+            // assert the content of the output file
+            def output_file = file(process.out.get(0).get(0).get(2))
+            def lines = output_file.readLines()
+            assert lines.size() == 1
+
+			assert lines[0] == "7 147730664 147738995 esv275461 duplication G <CN=2> 13 intron_variant 8331"
+		}
+	}
+
+	test("vcf_to_bed - --structural_variant not given for symbolic alts") {
+
+        when {
+            process {
+                """
+                input[0] = tuple([:], [:], file("${moduleDir}/tests/testdata/test_symbolic.vcf.gz"))
+                input[1] = "${projectDir}/assets/variation_consequnce_rank.json"
+                input[2] = "${projectDir}/assets/short_variant_bedfields.json"
+                input[3] = false
+                """
+            }
+        }
+
+		then {
+			assert process.failed
+			assert process.errorReport.contains("structural variant detected, but not running in structural variant mode")
+		}
+	}
 }
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test.snap
new file mode 100644
index 00000000..70a71f08
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/main.nf.test.snap
@@ -0,0 +1,24 @@
+{
+    "vcf_to_bed - --structural_variant for symbolic alts": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            
+                        },
+                        {
+                            
+                        },
+                        "test_symbolic.bed:md5,a4eb183fdc83377081994fb8f43374c5"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-03-03T10:37:19.99035"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz
new file mode 100644
index 00000000..9ff166a1
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz.tbi
new file mode 100644
index 00000000..7624d37a
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_symbolic.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz
new file mode 100644
index 00000000..654d73ce
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz.tbi b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz.tbi
new file mode 100755
index 00000000..504633ca
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vcf_to_bed/tests/testdata/test_vcftobed.vcf.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/cache/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/cache/main.nf
new file mode 100644
index 00000000..c37b7174
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/cache/main.nf
@@ -0,0 +1,62 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_CACHE_CONFIG {
+    cache false
+
+    input:
+    val genome_meta
+    val cache_meta
+    val version
+    val ini_file
+
+    output:
+    tuple val(genome_meta), path(cache_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    cache_config = "${prefix}.cache.txt"
+
+    active = cache_meta.active
+
+    genome_uuid = genome_meta.genome_uuid
+
+    cache_dir = cache_meta.dir ?: ""
+    
+    factory = cache_meta.factory ?: "old"
+    out_dir = genome_meta.genome_temp_dir ?: ""
+
+    ext_args = factory == "old" ?
+        "--species ${genome_meta.species} --assembly ${genome_meta.assembly} --version ${version}"
+        : ""
+
+    """
+    if [[ $active == 'false' ]]
+    then
+        echo '' > ${cache_config}
+    else
+        process_cache.py \
+            ${ext_args} \
+            --genome_uuid ${genome_uuid} \
+            --cache_dir ${cache_dir} \
+            --factory ${factory} \
+            --out_dir ${out_dir} \
+            --ini_file ${ini_file}
+    fi
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test
new file mode 100644
index 00000000..1649327b
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test
@@ -0,0 +1,151 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_CACHE_CONFIG"
+    script "../main.nf"
+    process "PROCESS_CACHE_CONFIG"
+
+    test("cache_dir - inactive") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['active':false]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+    
+    test("cache_dir - no cache") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                input[1] = ['dir':"${moduleDir}/tests"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("cache_dir - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                input[1] = ['dir':"${moduleDir}/tests/testdata"]
+                input[2] = 110
+                input[3] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                'species':'homo_sapiens', 
+                'assembly':'GRCh38'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("cache\t${moduleDir}/tests/testdata")
+            assert file_content.contains("cache_version\t110")
+        }
+    }
+
+    test("factory - no ini file") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [:]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("factory - old ftp") {
+
+        when {
+            process {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                input[0] = [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':tmp_dir
+                    ]
+                input[1] = [:]
+                input[2] = 110
+                input[3] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            
+            // genome_meta does not change
+            def tmp_dir = "${moduleDir}/tests/temp"
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                'species':'homo_sapiens', 
+                'assembly':'GRCh38',
+                'genome_temp_dir':tmp_dir
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("cache\t${tmp_dir}")
+            assert file_content.contains("cache_version\t110")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test.snap
new file mode 100644
index 00000000..37ce0af5
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "cache_dir - inactive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.cache.txt:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-10T11:24:41.997795"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/testdata/homo_sapiens/110_GRCh38/.gitkeep b/nextflow/vcf_prepper/modules/local/vep_config/cache/tests/testdata/homo_sapiens/110_GRCh38/.gitkeep
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/create/main.nf
new file mode 100644
index 00000000..cda07cff
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/create/main.nf
@@ -0,0 +1,54 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process CREATE_VEP_CONFIG {
+    cache false
+
+    // publishDir
+    //     out_dir
+
+    input:
+    tuple val(genome_meta),
+        path(default_options),
+        path(fasta_config),
+        path(gff_config),
+        path(cache_config),
+        path(plugins_config),
+        path(custom_annotation_config)
+
+    output:
+    tuple val(genome_meta), path(vep_config)
+
+    script:
+    def species = genome_meta.species
+    def assembly = genome_meta.assembly
+
+    def prefix = task.ext.prefix ?: "${species}_${assembly}"
+    vep_config = "${prefix}.ini"
+
+    """
+    cat \
+        ${default_options} \
+        ${fasta_config} \
+        ${gff_config} \
+        ${cache_config} \
+        ${plugins_config} \
+        ${custom_annotation_config} \
+        > ${vep_config}
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test
new file mode 100644
index 00000000..0682aa50
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test
@@ -0,0 +1,144 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process CREATE_VEP_CONFIG"
+    script "../main.nf"
+    process "CREATE_VEP_CONFIG"
+
+    test("cache inactive") {
+        setup {
+            run("PROCESS_DEFAULT_OPTIONS_CONFIG") {
+                script "../../default_options"
+
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = [force_overwrite:1, fork:2, vcf:1, spdi:1, variant_class:1, protein:1, transcript_version:1, gencode_promoter:1, offline:1]
+                    """
+                }
+            }
+
+            run("PROCESS_FASTA_CONFIG") {
+                script "../../fasta"
+
+                // not using factory because my local setting has issue with HTSlib
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = ['file':"${projectDir}/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz"]
+                    input[2] = 110
+                    input[3] = 'NONE'
+                    """
+                }
+            }
+
+            run("PROCESS_GFF_CONFIG") {
+                script "../../gff"
+
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = ['file':"${projectDir}/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz"]
+                    input[2] = 'NONE'
+                    """
+                }
+            }
+
+            run("PROCESS_CACHE_CONFIG") {
+                script "../../cache"
+
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = ['active':false]
+                    input[2] = 110
+                    input[3] = "${projectDir}/tests/testdata/test_db.ini"
+                    """
+                }
+            }
+
+            run("PROCESS_PLUGINS_CONFIG") {
+                script "../../plugins"
+
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = [conf:[[name:'CADD', keyed:true], [name:'SpliceAI', keyed:true]]]
+                    input[2] = 110
+                    input[3] = "${projectDir}"
+                    """
+                }
+            }
+
+            run("PROCESS_CUSTOM_ANNOTATIONS_CONFIG") {
+                script "../../custom_annotations"
+
+                process {
+                    """
+                    input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    input[1] = [:]
+                    input[2] = 110
+                    input[3] = "${projectDir}/assets/population_data.json"
+                    input[4] = true
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = Channel.of(['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38'])
+                    .combine(PROCESS_DEFAULT_OPTIONS_CONFIG.out, by:0)
+                    .combine(PROCESS_FASTA_CONFIG.out, by:0)
+                    .combine(PROCESS_GFF_CONFIG.out, by:0)
+                    .combine(PROCESS_CACHE_CONFIG.out, by:0)
+                    .combine(PROCESS_PLUGINS_CONFIG.out, by:0)
+                    .combine(PROCESS_CUSTOM_ANNOTATIONS_CONFIG.out, by:0)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                'species':'homo_sapiens', 
+                'assembly':'GRCh38'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("force_overwrite\t1")
+            assert file_content.contains("fork\t2")
+            assert file_content.contains("vcf\t1")
+            assert file_content.contains("spdi\t1")
+            assert file_content.contains("variant_class\t1")
+            assert file_content.contains("protein\t1")
+            assert file_content.contains("transcript_version\t1")
+            assert file_content.contains("gencode_promoter\t1")
+            assert file_content.contains("offline\t1")
+            assert file_content.contains("fasta\t${projectDir}/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz")
+            assert file_content.contains("gff\t${projectDir}/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz")
+            assert file_content.contains("plugin\tCADD,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz,indels=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz")
+            assert file_content.contains("plugin\tSpliceAI,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz,indel=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test.snap
new file mode 100644
index 00000000..cdb43e85
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/main.nf.test.snap
@@ -0,0 +1,23 @@
+{
+    "cache inactive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38"
+                        },
+                        "homo_sapiens_GRCh38.ini:md5,605cdf9693641626b6bbdb864c261b06"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-02-02T13:07:52.379294"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz
new file mode 100644
index 00000000..5700a622
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz
new file mode 100644
index 00000000..a984296b
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/create/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/main.nf
new file mode 100644
index 00000000..65df02f0
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/main.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_CUSTOM_ANNOTATIONS_CONFIG {
+    cache false
+
+    input:
+    val genome_meta 
+    val custom_annotation_meta
+    val version
+    val population_data_file
+    val skip_file_check
+
+    output:
+    tuple val(genome_meta), path(custom_annotations_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    custom_annotations_config = "${prefix}.custom_annotations.txt"
+
+    genome_uuid = genome_meta.genome_uuid
+    conf = custom_annotation_meta.conf ?: [:]
+    skip_file_check = skip_file_check ? "--skip_file_check" : ""
+
+    factory = custom_annotation_meta.factory ?: "old"
+
+    ext_args = factory == "old" ? 
+        "--species ${genome_meta.species} --assembly ${genome_meta.assembly} --version ${version} --population_data_file ${population_data_file}"
+        : ""
+
+	// convert custom annotation conf from groovy map to json file
+	custom_annotations_meta_json = new groovy.json.JsonBuilder(conf).toPrettyString()
+	conf = workDir + "/custom_annotations_conf.json"
+	file(conf).text = custom_annotations_meta_json
+
+    """
+    process_custom_annotations.py \
+        ${ext_args} \
+        --genome_uuid ${genome_uuid} \
+        --conf ${conf} \
+        ${skip_file_check}
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test
new file mode 100644
index 00000000..897c97bd
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test
@@ -0,0 +1,91 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_CUSTOM_ANNOTATIONS_CONFIG"
+    script "../main.nf"
+    process "PROCESS_CUSTOM_ANNOTATIONS_CONFIG"
+
+    test("conf - empty") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [:]
+                input[2] = 110
+                input[3] = 'NONE'
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            assert path(process.out.get(0).get(0).get(1)).text == ''
+        }
+    }
+
+    test("conf - empty 2") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['conf':[:]]
+                input[2] = 110
+                input[3] = 'NONE'
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            assert path(process.out.get(0).get(0).get(1)).text == ''
+        }
+    }
+
+    test("conf - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                input[1] = [conf:[[name:'frequency']]]
+                input[2] = 110
+                input[3] = "${projectDir}/assets/population_data.json"
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // genome_meta does not change
+            process.out.get(0).get(0).get(0) == ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']  
+
+            // contains custom annotation config
+            assert path(process.out.get(0).get(0).get(1)).getText().contains("gnomAD")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test.snap
new file mode 100644
index 00000000..1bb77322
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/custom_annotations/tests/main.nf.test.snap
@@ -0,0 +1,23 @@
+{
+    "conf - proper": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.custom_annotations.txt:md5,193c1fd9f8b84ba83372ec0c4b76b446"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-10T00:30:53.076579"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/default_options/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/default_options/main.nf
new file mode 100644
index 00000000..bc5bc632
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/default_options/main.nf
@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_DEFAULT_OPTIONS_CONFIG {
+    cache false
+
+    input:
+    val genome_meta
+    val default_options
+
+    output:
+    tuple val(genome_meta), path(default_options_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    default_options_config = "${prefix}.default_options.txt"
+
+    default_options_list = []
+    default_options.each {
+        option ->
+            default_options_list.add("${option.key}\t${option.value}")
+    }
+    default_options_str = default_options_list.join("\n")
+
+    """
+    # mv ${prefix}.temp.default_options.txt ${default_options_config}
+    cat > ${default_options_config}<< EOF
+${default_options_str}
+EOF
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test
new file mode 100644
index 00000000..65331635
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test
@@ -0,0 +1,42 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_DEFAULT_OPTIONS_CONFIG"
+    script "../main.nf"
+    process "PROCESS_DEFAULT_OPTIONS_CONFIG"
+
+    test("default_options") {
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [force_overwrite:1, fork:2, vcf:1, spdi:1, variant_class:1, protein:1, transcript_version:1, gencode_promoter:1, offline:1]
+                """
+            }
+        }
+        then {
+            println(process.success)
+            assert process.success
+            assert snapshot(process.out).match()
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test.snap
new file mode 100644
index 00000000..4433528b
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/default_options/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "default_options": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.default_options.txt:md5,a88593258ac2af4d24832fff8824e7a9"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-01-27T19:25:34.710224"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/fasta/main.nf
new file mode 100644
index 00000000..77572196
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/fasta/main.nf
@@ -0,0 +1,67 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_FASTA_CONFIG {
+    label 'process_medium'
+    cache false
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    val genome_meta
+    val fasta_meta
+    val version
+    val ini_file
+
+    output:
+    tuple val(genome_meta), path(fasta_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    fasta_config = "${prefix}.fasta.txt"
+
+    active = fasta_meta.active
+
+    genome_uuid = genome_meta.genome_uuid
+
+    fasta_file = fasta_meta.file ?: ""
+    fasta_dir = fasta_meta.dir ?: ""
+
+    factory = fasta_meta.factory ?: "current"
+    out_dir = genome_meta.genome_temp_dir ?: ""
+
+    ext_args = factory == "old"? 
+        "--species ${genome_meta.species} --assembly ${genome_meta.assembly} --version ${version}"
+        : ""
+
+    """
+    if [[ $active == 'false' ]]
+    then
+        echo '' > ${fasta_config}
+    else
+        process_fasta.py \
+            ${ext_args} \
+            --genome_uuid ${genome_uuid} \
+            --fasta_file ${fasta_file} \
+            --fasta_dir ${fasta_dir} \
+            --factory ${factory} \
+            --out_dir ${out_dir} \
+            --ini_file ${ini_file}
+    fi
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test
new file mode 100644
index 00000000..3bcadf45
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test
@@ -0,0 +1,277 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_FASTA_CONFIG"
+    script "../main.nf"
+    process "PROCESS_FASTA_CONFIG"
+
+    test("fasta_file - inactive") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['active':false]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+    
+    test("fasta_file - gzipped") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/unmasked_gzip.fa.gz"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("either not bgzipped or missing index")
+        }
+    }
+
+    test("fasta_file - no index") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/unmasked_bgzip_noindex.fa.gz"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("either not bgzipped or missing index")
+        }
+    }
+
+    test("fasta_file - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/unmasked.fa.gz"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("fasta\t${moduleDir}/tests/testdata/unmasked.fa.gz")
+        }
+    }
+
+    test("fasta_dir - no file") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['dir':"${moduleDir}/tests"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("fasta_dir - current factory") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['dir':"${moduleDir}/tests/testdata"]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("fasta\t${moduleDir}/tests/testdata/unmasked.fa.gz")
+        }
+    }
+
+    test("fasta_dir - old factory") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                input[1] = ['dir':"${moduleDir}/tests/testdata", 'factory':'old']
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                'species':'homo_sapiens', 
+                'assembly':'GRCh38'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("fasta\t${moduleDir}/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz")
+        }
+    }
+
+    test("factory - no ini file") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [:]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("factory - new ftp") {
+
+        when {
+            process {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                input[0] = [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                        'genome_temp_dir':tmp_dir
+                    ]
+                input[1] = [:]
+                input[2] = 110
+                input[3] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            def tmp_dir = "${moduleDir}/tests/temp"
+            assert process.out.get(0).get(0).get(0) == [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                        'genome_temp_dir':tmp_dir
+                    ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("fasta\t${tmp_dir}/unmasked.fa.gz")
+        }
+    }
+
+    test("factory - old ftp") {
+
+        when {
+            process {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                input[0] = [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':tmp_dir
+                    ]
+                input[1] = ['factory':'old']
+                input[2] = 110
+                input[3] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            def tmp_dir = "${moduleDir}/tests/temp"
+            assert process.out.get(0).get(0).get(0) == [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':tmp_dir
+                    ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("fasta\t${tmp_dir}/Homo_sapiens.GRCh38.dna.toplevel.fa.gz")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test.snap
new file mode 100644
index 00000000..5654f59c
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "fasta_file - inactive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.fasta.txt:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-10T10:56:16.226607"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai
new file mode 100644
index 00000000..82326ef1
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai
@@ -0,0 +1 @@
+1	780	46	60	61
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.gzi b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.gzi
new file mode 100644
index 00000000..0423f675
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.gzi differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.fai b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.fai
new file mode 100644
index 00000000..82326ef1
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.fai
@@ -0,0 +1 @@
+1	780	46	60	61
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.gzi b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.gzi
new file mode 100644
index 00000000..0423f675
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz.gzi differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_bgzip_noindex.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_bgzip_noindex.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_bgzip_noindex.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_gzip.fa.gz b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_gzip.fa.gz
new file mode 100644
index 00000000..63a70c14
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/fasta/tests/testdata/unmasked_gzip.fa.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/gff/main.nf
new file mode 100644
index 00000000..65633161
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/gff/main.nf
@@ -0,0 +1,61 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_GFF_CONFIG {
+    label 'process_medium'
+    cache false
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    val genome_meta
+    val gff_meta
+    val ini_file
+
+    output:
+    tuple val(genome_meta), path(gff_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    gff_config = "${prefix}.gff.txt"
+
+    active = gff_meta.active
+
+    genome_uuid = genome_meta.genome_uuid
+
+    gff_file = gff_meta.file ?: ""
+    gff_dir = gff_meta.dir ?: ""
+
+    factory = gff_meta.factory ?: "current"
+    out_dir = genome_meta.genome_temp_dir ?: ""
+
+    """
+    if [[ $active == 'false' ]]
+    then
+        echo '' > ${gff_config}
+    else
+        process_gff.py \
+            --genome_uuid ${genome_uuid} \
+            --gff_file ${gff_file} \
+            --gff_dir ${gff_dir} \
+            --factory ${factory} \
+            --out_dir ${out_dir} \
+            --ini_file ${ini_file}
+    fi
+    """
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test
new file mode 100644
index 00000000..69bc2c05
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test
@@ -0,0 +1,200 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_GFF_CONFIG"
+    script "../main.nf"
+    process "PROCESS_GFF_CONFIG"
+
+    test("gff_file - inactive") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['active':false]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("gff_file - gzipped") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/genes_gzip.gff3.gz"]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("either not bgzipped or missing tabix index")
+        }
+    }
+
+    test("gff_file - no index") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/genes_bgzip_noindex.gff3.gz"]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("either not bgzipped or missing tabix index")
+        }
+    }
+
+    test("gff_file - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['file':"${moduleDir}/tests/testdata/genes.gff3.gz"]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success   
+            
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("gff\t${moduleDir}/tests/testdata/genes.gff3.gz")        
+        }
+    }
+
+    test("gff_dir - no file") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['dir':"${moduleDir}/tests"]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("gff_dir - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = ['dir':"${moduleDir}/tests/testdata"]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("gff\t${moduleDir}/tests/testdata/genes.gff3.gz")
+        }
+    }
+
+    test("factory - no ini file") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [:]
+                input[2] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.failed
+            assert process.errorReport.contains("FileNotFoundError")
+        }
+    }
+
+    test("factory - new ftp") {
+
+        when {
+            process {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                input[0] = [
+                    'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                    'genome_temp_dir':tmp_dir
+                ]
+                input[1] = [:]
+                input[2] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            def tmp_dir = "${moduleDir}/tests/temp"
+            assert process.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                'genome_temp_dir':tmp_dir
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text
+            assert file_content.contains("gff\t${tmp_dir}/sorted_genes.gff3.gz")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test.snap
new file mode 100644
index 00000000..496336e9
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "gff_file - inactive": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.gff.txt:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-10T10:39:21.548777"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz
new file mode 100644
index 00000000..5700a622
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz
new file mode 100644
index 00000000..afb869e7
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz.tbi b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz.tbi
new file mode 100644
index 00000000..20e09d4d
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz.tbi differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_bgzip_noindex.gff3.gz b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_bgzip_noindex.gff3.gz
new file mode 100644
index 00000000..6ca4ec83
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_bgzip_noindex.gff3.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_gzip.gff3.gz b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_gzip.gff3.gz
new file mode 100644
index 00000000..07db1369
Binary files /dev/null and b/nextflow/vcf_prepper/modules/local/vep_config/gff/tests/testdata/genes_gzip.gff3.gz differ
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/main.nf b/nextflow/vcf_prepper/modules/local/vep_config/plugins/main.nf
new file mode 100644
index 00000000..c328ae4c
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/plugins/main.nf
@@ -0,0 +1,55 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process PROCESS_PLUGINS_CONFIG {
+    cache false
+
+    input:
+    val genome_meta
+    val plugins_meta
+    val version
+    val repo_dir        // can we make it optional? using ext.args and nextflow.config
+
+    output:
+    tuple val(genome_meta), path(plugins_config)
+
+    script:
+    def prefix = task.ext.prefix ?: "${genome_meta.genome_uuid}"
+    plugins_config = "${prefix}.plugins.txt"
+
+    genome_uuid = genome_meta.genome_uuid
+    conf = plugins_meta.conf ?: [:]
+
+    factory = plugins_meta.factory ?: "old"
+    ext_args = factory == "old" ?
+        "--species ${genome_meta.species} --assembly ${genome_meta.assembly} --version ${version}"
+        : ""
+
+	// convert plugin conf from groovy map to json file
+	plugin_meta_json = new groovy.json.JsonBuilder(conf).toPrettyString()
+	conf = workDir + "/plugin_conf.json"
+	file(conf).text = plugin_meta_json
+
+    """
+    process_vep_plugins.py \
+        ${ext_args} \
+        --genome_uuid ${genome_uuid} \
+        --conf ${conf} \
+        --repo_dir ${repo_dir}
+    """
+}
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test
new file mode 100644
index 00000000..59828b41
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test
@@ -0,0 +1,89 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test process PROCESS_PLUGINS_CONFIG"
+    script "../main.nf"
+    process "PROCESS_PLUGINS_CONFIG"
+
+    test("conf - empty") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [:]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            assert path(process.out.get(0).get(0).get(1)).text == ''
+        }
+    }
+
+    test("conf - empty 2") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb']
+                input[1] = [conf:[:]]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            assert path(process.out.get(0).get(0).get(1)).text == ''
+        }
+    }
+
+    test("conf - proper") {
+
+        when {
+            process {
+                """
+                input[0] = ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                input[1] = [conf:[[name:'CADD', keyed:true], [name:'SpliceAI', keyed:true]]]
+                input[2] = 110
+                input[3] = 'NONE'
+                """
+            }
+        }
+
+        then {
+            assert process.success
+
+            // genome_meta does not change
+            assert process.out.get(0).get(0).get(0) == ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+            
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(process.out.get(0).get(0).get(1)).text    
+            assert file_content.contains("plugin\tCADD,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz,indels=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz")
+            assert file_content.contains("plugin\tSpliceAI,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz,indel=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test.snap
new file mode 100644
index 00000000..5afdfe87
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/main.nf.test.snap
@@ -0,0 +1,23 @@
+{
+    "conf - proper": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38"
+                        },
+                        "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb.plugins.txt:md5,858cfa31299d29e750ad7264ac09b0b8"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-09T00:27:20.509451"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz b/nextflow/vcf_prepper/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig.nf b/nextflow/vcf_prepper/modules/local/wig_to_bigwig.nf
deleted file mode 100755
index 601a1cad..00000000
--- a/nextflow/vcf_prepper/modules/local/wig_to_bigwig.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env nextflow
-
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-process WIG_TO_BIGWIG {
-  input: 
-  tuple val(meta), path(wig)
-  
-  output:
-  path "variant-${source}-summary.bw"
-  
-  memory  { (wig.size() * 10.B + 1.GB) * task.attempt }
-  time    { 48.hour * task.attempt }
-  
-  shell:
-  source = meta.source.toLowerCase()
-  output_bw = "${meta.genome_tracks_outdir}/variant-${source}-summary.bw"
-  chrom_sizes = meta.chrom_sizes
-  
-  '''
-  wigToBigWig -clip -keepAllChromosomes -fixedSummaries \
-    !{wig} \
-    !{chrom_sizes} \
-    !{output_bw}
-    
-  ln -sf !{output_bw} "variant-!{source}-summary.bw"
-  
-  # temp: for one source we create symlink for focus if only one source present
-  if [[ ! !{meta.multiple_source} ]]
-  then
-    cd !{meta.genome_tracks_outdir}
-    ln -sf variant-!{source}-summary.bw variant-summary.bw
-  fi
-  '''
-}
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig/main.nf b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/main.nf
new file mode 100755
index 00000000..09e540dc
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/main.nf
@@ -0,0 +1,50 @@
+#!/usr/bin/env nextflow
+
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+process WIG_TO_BIGWIG {
+	memory { (wig.size() * 7.B + 1.GB) * task.attempt }
+	time { 2.hour * task.attempt }
+
+	input:
+	tuple val(genome_meta), val(file_meta), path(wig)
+
+	output:
+	path "variant-${source}-summary.bw"
+
+	script:
+	source = file_meta.source.toLowerCase()
+	output_bw = "${genome_meta.genome_tracks_outdir}/variant-${source}-summary.bw"
+	chrom_sizes = genome_meta.chrom_sizes_file
+
+	"""
+	wigToBigWig -clip -keepAllChromosomes -fixedSummaries \
+		${wig} \
+		${chrom_sizes} \
+		${output_bw}
+
+	# for the purpose of output and caching
+	ln -sf ${output_bw} "variant-${source}-summary.bw"
+	
+	# temp: for one source we create symlink for focus if only one source present
+	if [[ "${file_meta.multiple_source}" == "false" ]]
+	then
+		cd ${genome_meta.genome_tracks_outdir}
+		ln -sf variant-${source}-summary.bw variant-summary.bw
+	fi
+	"""
+}
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test
new file mode 100644
index 00000000..e253a24a
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test
@@ -0,0 +1,60 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_process {
+
+    name "Test Process WIG_TO_BIGWIG"
+    script "../main.nf"
+    process "WIG_TO_BIGWIG"
+
+    test("wig_to_bigwig") {
+
+        when {
+            process {
+                """
+				// use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+                
+				genome_meta = [:]
+                genome_meta["source"] = "test"
+				genome_meta["chrom_sizes_file"] = file("${moduleDir}/tests/testdata/homo_sapiens_GRCh38.chrom.sizes")
+				genome_meta["genome_tracks_outdir"] = tmp_dir
+
+				file_meta = [:]
+                file_meta["source"] = "test"
+                file_meta["multiple_source"] = false
+
+				input[0] = tuple(genome_meta, file_meta, file("${moduleDir}/tests/testdata/short_variants.wig"))
+                """
+            }
+        }
+
+        then {
+            assert process.success 
+            assert snapshot(process.out).match()
+            
+            // the output is generated at the genome tracks dir
+			// assert for single source we symlink the focus track
+            def tmp_dir = "${moduleDir}/tests/temp"
+			assert file(tmp_dir + "/variant-test-summary.bw").exists()
+			assert file(tmp_dir + "/variant-summary.bw").exists()
+			assert file(tmp_dir + "/variant-summary.bw").getCanonicalPath() == 
+				(projectDir + "/modules/local/wig_to_bigwig/tests/temp/variant-test-summary.bw")
+		}
+    }
+}
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test.snap b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test.snap
new file mode 100644
index 00000000..389e5060
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "wig_to_bigwig": {
+        "content": [
+            {
+                "0": [
+                    "variant-test-summary.bw:md5,d7c4b877e112de820926797cb211bad8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-12-24T22:03:16.698301"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/homo_sapiens_GRCh38.chrom.sizes b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/homo_sapiens_GRCh38.chrom.sizes
new file mode 100755
index 00000000..afae07a7
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/homo_sapiens_GRCh38.chrom.sizes
@@ -0,0 +1,2 @@
+2	242193530
+1	248956423
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/short_variants.wig b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/short_variants.wig
new file mode 100644
index 00000000..7d049d93
--- /dev/null
+++ b/nextflow/vcf_prepper/modules/local/wig_to_bigwig/tests/testdata/short_variants.wig
@@ -0,0 +1,514 @@
+fixedStep  chrom=1 start=1 step=1
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
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+0
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+0
+0
+3
+0
+1
+0
+0
+0
+0
+0
+0
+0
+0
+1
+fixedStep  chrom=2 start=1 step=1
+0
+0
+0
+0
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diff --git a/nextflow/vcf_prepper/nextflow.config b/nextflow/vcf_prepper/nextflow.config
index fa6488b5..e9ebfb42 100755
--- a/nextflow/vcf_prepper/nextflow.config
+++ b/nextflow/vcf_prepper/nextflow.config
@@ -1,139 +1,181 @@
-trace.overwrite = true
-dag.overwrite = true
+nextflowVersion = '!>=23.10.0'
 
 params {
-  // Ensembl version and release id
-  version = 108
-  release_id = 6
-  
-  // Ensembl repositories
-  repo_dir = "/hps/software/users/ensembl/variation/${USER}"
-
-  // config files
-  input_config = "${projectDir}/assets/input_sources.json"
-  ini_file = "${projectDir}/assets/DEFAULT.ini"
-  rank_file = "${projectDir}/assets/variation_consequnce_rank.json"
-  population_data_file = null
-  sources_meta_file = "${projectDir}/assets/sources_meta.json"
-  
-  // data directories
-  cache_dir = null
-  gff_dir = null
-  fasta_dir = null
-  conservation_data_dir = null
-  
-  // output dir
-  output_dir = "/nfs/production/flicek/ensembl/variation/new_website"
-  temp_dir = params.output_dir + "/tmp"
-  
-  // pipeline control parameters
-  structural_variant = 0
-  use_old_infra = 1
-  use_vep_cache = 1
-  bin_size = 250000
-  remove_nonunique_ids = 0
-  remove_patch_regions = 1
-  skip_vep = 0
-  skip_tracks = 0
-  skip_stats = 0
-  force_create_config = 0
-  rename_clinvar_ids = 1
-  queue_size = 1200
-  queue = 'production'
+	// Ensembl version and release id
+	version = 110
+	release_id = 6
+
+	// Ensembl repositories
+	repo_dir = null
+
+	// output dir
+	output_dir = "${launchDir}"
+	temp_dir = params.output_dir + "/tmp"
+
+	// config files
+	input_config = null
+	vep_config = "${projectDir}/assets/vep_config.json"
+	ini_file = null
+    synonym_file = null
+	chrom_sizes_file = null
+	rank_file = "${projectDir}/assets/variation_consequnce_rank.json"
+	population_data_file = !params.structural_variant ? "${projectDir}/assets/population_data.json" : null
+	sources_meta_file = "${projectDir}/assets/sources_meta.json"
+	bed_fields = "${projectDir}/assets/short_variant_bedfields.json"
+
+	// // global VEP annotation source parameters
+	// cache {
+	//     active = true
+	//     dir = null
+	//     factory = "old_ftp"
+	// }
+	// fasta {
+	//     active = true
+	//     dir = null
+	//     file = null
+	//     factory = "old_ftp"
+	// }
+	// gff {
+	//     active = false
+	//     dir = null
+	//     file = null
+	//     factory = "new_ftp"
+	// }
+
+	// // global VEP plugins parameters
+	// vep_plugins {
+	//     file_factory = "old_ftp"
+	//     genome_matcher = null
+	// }
+
+	// // global VEP custom annotation parameters
+	// custom_annotations {
+	//     file_factory = "new_ftp"
+	//     genome_matcher = null
+	// }
+
+	// pipeline control parameters
+	structural_variant = 0
+	bin_size = 250000
+	remove_nonunique_ids = 0
+	remove_patch_regions = 1
+	skip_vep = 0
+	skip_tracks = 0
+	skip_stats = 0
+	rename_clinvar_ids = 1
+	queue_size = 1200
+	queue = 'production'
+}
+
+
+plugins {
+	id 'nf-schema@2.2.0'
+}
+
+validation {
+	help {
+		enabled = true
+	}
 }
 
 profiles {
-  standard {
-    executor.name = 'local'
-  }
+	standard {
+		executor.name = 'local'
+	}
 
-  lsf {
-    executor.name = 'lsf'
-  }
+	lsf {
+		executor.name = 'lsf'
+	}
 
-  slurm {
-    executor.name = 'slurm'
-  } 
+	slurm {
+		executor.name = 'slurm'
+	}
 }
 
 process {
-  cpus    = 1
-  memory  = { 2.GB * task.attempt }
-  time    = { 12.hour * task.attempt }
-  queue   = params.queue
-
-  // error strategy
-  errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-  maxRetries    = 1
-
-  withLabel: process_low {
-    memory  = { 1.GB * task.attempt }
-    time    = { 1.hour * task.attempt }
-  }
-  
-  withLabel: process_medium {
-    cpus    = { 1 * task.attempt }
-    memory  = { 4.GB * task.attempt }
-    time    = { 24.hour * task.attempt }
-  }
-
-  withLabel: process_high {
-    cpus    = { 1 * task.attempt }
-    memory  = { 8.GB * task.attempt }
-    time    = { 48.hour * task.attempt }
-  }
-  
-  withName: 'runVEPonVCF'{
-    cpus    = { 2 * task.attempt }
-    memory  = { 96.KB * params.bin_size * task.attempt + 1.GB }
-    time    = { 0.00008.hour * params.bin_size * task.attempt + 1.hour }
-  }
-
-  withName: 'mergeVCF'{
-    cpus    = { 1 * task.attempt }
-    memory  = { 4.GB * task.attempt }
-    time    = { 48.hour * task.attempt }
-  }
-
-  withLabel: bcftools {
-    container = 'docker://quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
-  }
-
-  withLabel: vep {
-    container = 'docker://ensemblorg/ensembl-vep'
-  }
+	cpus = 1
+	memory = { 2.GB * task.attempt }
+	time = { 12.hour * task.attempt }
+	queue = params.queue
+
+	// error strategy
+	errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+	maxRetries = 1
+
+	withLabel: process_low {
+		memory = { 1.GB * task.attempt }
+		time = { 1.hour * task.attempt }
+	}
+
+	withLabel: process_medium {
+		cpus = { 1 * task.attempt }
+		memory = { 4.GB * task.attempt }
+		time = { 24.hour * task.attempt }
+	}
+
+	withLabel: process_high {
+		cpus = { 1 * task.attempt }
+		memory = { 8.GB * task.attempt }
+		time = { 48.hour * task.attempt }
+	}
+
+	withName: BED_TO_BIGBED {
+		cpus = { 1 * task.attempt }
+		memory = { 15.GB * task.attempt }
+		time = { 3.hour * task.attempt }
+	}
+
+	withName: runVEPonVCF {
+		cpus = { 2 * task.attempt }
+		memory = { 10.KB * params.bin_size * task.attempt + 1.GB }
+		time = { 0.00008.hour * params.bin_size * task.attempt + 1.hour }
+	}
+
+	withName: mergeVCF {
+		cpus = { 1 * task.attempt }
+		memory = { 4.GB * task.attempt }
+		time = { 48.hour * task.attempt }
+	}
+
+	withLabel: bcftools {
+		container = 'docker://quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
+	}
+
+	withLabel: vep {
+		container = 'docker://ensemblorg/ensembl-vep'
+	}
 }
 
 executor {
-  queueSize = params.queue_size
-  submitRateLimit = '50/10sec'
+	queueSize = params.queue_size
+	submitRateLimit = '50/10sec'
 }
 
 singularity {
-  enabled = true
-  autoMounts = true
+	enabled = true
+	autoMounts = true
 }
 
 trace {
-    enabled = true
-    overwrite = true
-    file = "reports/trace.txt"
+	enabled = true
+	overwrite = true
+	file = "reports/trace.txt"
 }
 
 dag {
-    enabled = true
-    overwrite = true
-    file = "reports/flowchart.mmd"
+	enabled = true
+	overwrite = true
+	file = "reports/flowchart.mmd"
 }
 
 timeline {
-    enabled = true
-    overwrite = true
-    file = "reports/timeline.html"
+	enabled = true
+	overwrite = true
+	file = "reports/timeline.html"
 }
 
 report {
-    enabled = true
-    overwrite = true
-    file = "reports/report.html"
-}
\ No newline at end of file
+	enabled = true
+	overwrite = true
+	file = "reports/report.html"
+}
diff --git a/nextflow/vcf_prepper/nextflow_schema.json b/nextflow/vcf_prepper/nextflow_schema.json
new file mode 100644
index 00000000..426753c3
--- /dev/null
+++ b/nextflow/vcf_prepper/nextflow_schema.json
@@ -0,0 +1,129 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema",
+  "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+  "title": ". pipeline parameters",
+  "description": "",
+  "type": "object",
+  "definitions": {
+    "generic_options": {
+      "title": "Generic options",
+      "type": "object",
+      "fa_icon": "fas fa-file-import",
+      "description": "Less common options for the pipeline, typically set in a config file.",
+      "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+      "properties": {
+        "version": {
+          "type": "boolean",
+          "description": "Display version and exit.",
+          "fa_icon": "fas fa-question-circle",
+          "default": false,
+          "hidden": true
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/definitions/generic_options"
+    }
+  ],
+  "properties": {
+    "release_id": {
+      "type": "integer",
+      "default": 6
+    },
+    "repo_dir": {
+      "type": "string",
+      "default": "None"
+    },
+    "input_config": {
+      "type": "string",
+      "default": "${projectDir}/assets/input_sources.json"
+    },
+    "ini_file": {
+      "type": "string",
+      "default": "${projectDir}/assets/DEFAULT.ini"
+    },
+    "rank_file": {
+      "type": "string",
+      "default": "${projectDir}/assets/variation_consequnce_rank.json"
+    },
+    "population_data_file": {
+      "type": "string",
+      "default": "None"
+    },
+    "sources_meta_file": {
+      "type": "string",
+      "default": "${projectDir}/assets/sources_meta.json"
+    },
+    "output_dir": {
+      "type": "string",
+      "default": "${launchDir}"
+    },
+    "temp_dir": {
+      "type": "string",
+      "default": "${launchDir}/tmp"
+    },
+    "structural_variant": {
+      "type": "integer",
+      "default": 0
+    },
+    "bin_size": {
+      "type": "integer",
+      "default": 250000
+    },
+    "remove_nonunique_ids": {
+      "type": "integer",
+      "default": 0
+    },
+    "remove_patch_regions": {
+      "type": "integer",
+      "default": 1
+    },
+    "skip_vep": {
+      "type": "integer",
+      "default": 0
+    },
+    "skip_tracks": {
+      "type": "integer",
+      "default": 0
+    },
+    "skip_stats": {
+      "type": "integer",
+      "default": 0
+    },
+    "force_create_config": {
+      "type": "integer",
+      "default": 0
+    },
+    "rename_clinvar_ids": {
+      "type": "integer",
+      "default": 1
+    },
+    "queue_size": {
+      "type": "integer",
+      "default": 1200
+    },
+    "queue": {
+      "type": "string",
+      "default": "production"
+    },
+    "vep_config": {
+      "type": "string",
+      "default": "${projectDir}/assets/vep_config.json"
+    },
+    "synonym_file": {
+      "type": "string",
+      "default": "None"
+    },
+    "chrom_sizes_file": {
+      "type": "string",
+      "default": "None"
+    },
+    "bed_fields": {
+      "type": "string",
+      "default": "${projectDir}/assets/short_variant_bedfields.json"
+    }
+  },
+  "required": ["repo_dir"]
+}
diff --git a/nextflow/vcf_prepper/nf-test.config b/nextflow/vcf_prepper/nf-test.config
index 870799df..fe1f62ad 100755
--- a/nextflow/vcf_prepper/nf-test.config
+++ b/nextflow/vcf_prepper/nf-test.config
@@ -1,8 +1,11 @@
 config {
-
-    testsDir "tests"
+	testsDir "tests"
     workDir ".nf-test"
     configFile "tests/nextflow.config"
-    profile ""
+    profile "local"
+	triggers "nextflow.config", "nf-test.config"
 
+	plugins {
+    	load "nft-vcf@1.0.7"
+    }
 }
diff --git a/nextflow/vcf_prepper/nf-test.txt b/nextflow/vcf_prepper/nf-test.txt
new file mode 100644
index 00000000..6baaac35
--- /dev/null
+++ b/nextflow/vcf_prepper/nf-test.txt
@@ -0,0 +1,21 @@
+
+🚀 nf-test 0.9.2
+https://www.nf-test.com
+(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr
+
+Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar
+nf-test runs in CI mode.
+
+Test process FORMAT_VCF
+
+  Test [5b80a892] 'remove criteria - all' PASSED (4.059s)
+  Test [6f3545b8] 'remove criteria - non-unique ids' PASSED (3.808s)
+  Test [47544e8a] 'remove criteria - patch regions' PASSED (3.765s)
+  Test [6f793deb] 'remove criteria - none' PASSED (3.798s)
+  Test [2a06e1db] 'multiple source' PASSED (3.695s)
+  Test [cf070d74] 'SV fields - SVLEN and END' PASSED (3.696s)
+  Test [b6fe7027] 'HGSVC field - NODEID' PASSED (3.671s)
+
+
+SUCCESS: Executed 7 tests in 26.529s
+
diff --git a/nextflow/vcf_prepper/requirements.txt b/nextflow/vcf_prepper/requirements.txt
new file mode 100644
index 00000000..827819eb
--- /dev/null
+++ b/nextflow/vcf_prepper/requirements.txt
@@ -0,0 +1,4 @@
+cyvcf2==0.31.1
+Deprecated>=1.2.18
+pylint>=2.9.6
+biopython>=1.81
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.lock b/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.lock
deleted file mode 100755
index a6d9ef27..00000000
--- a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.lock
+++ /dev/null
@@ -1,175 +0,0 @@
-# This file is automatically @generated by Cargo.
-# It is not intended for manual editing.
-version = 3
-
-[[package]]
-name = "adler"
-version = "1.0.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
-
-[[package]]
-name = "cfg-if"
-version = "1.0.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
-
-[[package]]
-name = "crc32fast"
-version = "1.3.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d"
-dependencies = [
- "cfg-if",
-]
-
-[[package]]
-name = "flate2"
-version = "1.0.25"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a8a2db397cb1c8772f31494cb8917e48cd1e64f0fa7efac59fbd741a0a8ce841"
-dependencies = [
- "crc32fast",
- "miniz_oxide",
-]
-
-[[package]]
-name = "itoa"
-version = "1.0.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6"
-
-[[package]]
-name = "memchr"
-version = "2.5.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d"
-
-[[package]]
-name = "minimal-lexical"
-version = "0.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
-
-[[package]]
-name = "miniz_oxide"
-version = "0.6.2"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b275950c28b37e794e8c55d88aeb5e139d0ce23fdbbeda68f8d7174abdf9e8fa"
-dependencies = [
- "adler",
-]
-
-[[package]]
-name = "nom"
-version = "7.1.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
-dependencies = [
- "memchr",
- "minimal-lexical",
-]
-
-[[package]]
-name = "once_cell"
-version = "1.17.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b7e5500299e16ebb147ae15a00a942af264cf3688f47923b8fc2cd5858f23ad3"
-
-[[package]]
-name = "proc-macro2"
-version = "1.0.51"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5d727cae5b39d21da60fa540906919ad737832fe0b1c165da3a34d6548c849d6"
-dependencies = [
- "unicode-ident",
-]
-
-[[package]]
-name = "quote"
-version = "1.0.23"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8856d8364d252a14d474036ea1358d63c9e6965c8e5c1885c18f73d70bff9c7b"
-dependencies = [
- "proc-macro2",
-]
-
-[[package]]
-name = "ryu"
-version = "1.0.13"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f91339c0467de62360649f8d3e185ca8de4224ff281f66000de5eb2a77a79041"
-
-[[package]]
-name = "serde"
-version = "1.0.152"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bb7d1f0d3021d347a83e556fc4683dea2ea09d87bccdf88ff5c12545d89d5efb"
-
-[[package]]
-name = "serde_json"
-version = "1.0.94"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1c533a59c9d8a93a09c6ab31f0fd5e5f4dd1b8fc9434804029839884765d04ea"
-dependencies = [
- "itoa",
- "ryu",
- "serde",
-]
-
-[[package]]
-name = "syn"
-version = "1.0.109"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
-dependencies = [
- "proc-macro2",
- "quote",
- "unicode-ident",
-]
-
-[[package]]
-name = "thiserror"
-version = "1.0.38"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6a9cd18aa97d5c45c6603caea1da6628790b37f7a34b6ca89522331c5180fed0"
-dependencies = [
- "thiserror-impl",
-]
-
-[[package]]
-name = "thiserror-impl"
-version = "1.0.38"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1fb327af4685e4d03fa8cbcf1716380da910eeb2bb8be417e7f9fd3fb164f36f"
-dependencies = [
- "proc-macro2",
- "quote",
- "syn",
-]
-
-[[package]]
-name = "unicode-ident"
-version = "1.0.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "84a22b9f218b40614adcb3f4ff08b703773ad44fa9423e4e0d346d5db86e4ebc"
-
-[[package]]
-name = "vcf"
-version = "0.6.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "40afbbcfe14b8c3bdaddc8bba0cb32e1d0f2b0b0196a8633ac37a7a000b88035"
-dependencies = [
- "nom",
- "once_cell",
- "thiserror",
-]
-
-[[package]]
-name = "vcf_to_bed"
-version = "0.1.0"
-dependencies = [
- "flate2",
- "serde_json",
- "vcf",
-]
diff --git a/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/main.nf b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/main.nf
new file mode 100644
index 00000000..46d455b0
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/main.nf
@@ -0,0 +1,61 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+include { PROCESS_FASTA_CONFIG } from "../../../modules/local/vep_config/fasta"
+include { PROCESS_GFF_CONFIG } from "../../../modules/local/vep_config/gff"
+include { PROCESS_CACHE_CONFIG } from "../../../modules/local/vep_config/cache"
+include { PROCESS_DEFAULT_OPTIONS_CONFIG } from "../../../modules/local/vep_config/default_options"
+include { PROCESS_PLUGINS_CONFIG } from "../../../modules/local/vep_config/plugins"
+include { PROCESS_CUSTOM_ANNOTATIONS_CONFIG } from "../../../modules/local/vep_config/custom_annotations"
+include { CREATE_VEP_CONFIG } from "../../../modules/local/vep_config/create"
+
+workflow GENERATE_VEP_CONFIG {
+  take:
+    genome_meta                     // channel: [ val(genome_meta) ]
+    fasta                           //     map: fasta conf 
+    gff                             //     map: gff conf
+    vep_cache                       //     map: cache conf
+    default_options                 //     map: default options conf
+    vep_plugins                     //     map: VEP plugins conf
+    custom_annotations              //     map: custom annotations conf
+    ini_file                        //     str: INI file with database connection info
+    version                         //     int: Ensembl (old) release version / schema version
+    release_id                      //     int: Ensembl release id
+    repo_dir                        //     str: path to Ensembl repositories
+    population_data_file            //     str: path to population_data.json
+
+  
+  main:
+    PROCESS_FASTA_CONFIG( genome_meta, fasta, version, ini_file )
+    PROCESS_GFF_CONFIG( genome_meta, gff, ini_file )
+    PROCESS_CACHE_CONFIG( genome_meta, vep_cache, version, ini_file )
+    PROCESS_DEFAULT_OPTIONS_CONFIG( genome_meta, default_options )
+    PROCESS_PLUGINS_CONFIG( genome_meta, vep_plugins, version, repo_dir )
+    PROCESS_CUSTOM_ANNOTATIONS_CONFIG( genome_meta, custom_annotations, version, population_data_file, false )
+
+    CREATE_VEP_CONFIG(
+        genome_meta
+            .combine(PROCESS_DEFAULT_OPTIONS_CONFIG.out, by:0)
+            .combine(PROCESS_FASTA_CONFIG.out, by:0)
+            .combine(PROCESS_GFF_CONFIG.out, by:0)
+            .combine(PROCESS_CACHE_CONFIG.out, by:0)
+            .combine(PROCESS_PLUGINS_CONFIG.out, by:0)
+            .combine(PROCESS_CUSTOM_ANNOTATIONS_CONFIG.out, by:0)
+    )
+
+  emit:
+    CREATE_VEP_CONFIG.out
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test
new file mode 100644
index 00000000..8dc539de
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test
@@ -0,0 +1,74 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_workflow {
+
+    name "Test workflow GENERATE_VEP_CONFIG"
+    script "../main.nf"
+    workflow "GENERATE_VEP_CONFIG"
+
+    test("generate_vep_config") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.fromList([
+                        ['genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 'species':'homo_sapiens', 'assembly':'GRCh38']
+                    ])
+                input[1] = ['file':"${projectDir}/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz"]
+                input[2] = ['file':"${projectDir}/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz"]
+                input[3] = ['active':false]
+                input[4] = [force_overwrite:1, fork:2, vcf:1, spdi:1, variant_class:1, protein:1, transcript_version:1, gencode_promoter:1, offline:1]
+                input[5] = [conf:[[name:'CADD', keyed:true], [name:'SpliceAI', keyed:true]]]
+                input[6] = [:]
+                input[7] = "${projectDir}/tests/testdata/test_db.ini"
+                input[8] = 110
+                input[9] = 'NONE'
+                input[10] = 'NONE'
+                input[11] = "${projectDir}/assets/population_data.json"
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            // genome_meta does not change
+            assert workflow.out.get(0).get(0).get(0) == [
+                'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb', 
+                'species':'homo_sapiens', 
+                'assembly':'GRCh38'
+            ]
+
+            // cannot do snapshot match as cache dir path may vary 
+            def file_content = path(workflow.out.get(0).get(0).get(1)).text
+            assert file_content.contains("force_overwrite\t1")
+            assert file_content.contains("fork\t2")
+            assert file_content.contains("vcf\t1")
+            assert file_content.contains("spdi\t1")
+            assert file_content.contains("variant_class\t1")
+            assert file_content.contains("protein\t1")
+            assert file_content.contains("transcript_version\t1")
+            assert file_content.contains("gencode_promoter\t1")
+            assert file_content.contains("offline\t1")
+            assert file_content.contains("fasta\t${projectDir}/modules/local/vep_config/fasta/tests/testdata/unmasked.fa.gz")
+            assert file_content.contains("gff\t${projectDir}/modules/local/vep_config/gff/tests/testdata/genes.gff3.gz")
+            assert file_content.contains("plugin\tCADD,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz,indels=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz")
+            assert file_content.contains("plugin\tSpliceAI,snv=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz,indel=${projectDir}/modules/local/vep_config/plugins/tests/testdata/grch38/e113/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz")
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test.snap b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test.snap
new file mode 100644
index 00000000..29310de7
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/generate_vep_config/tests/main.nf.test.snap
@@ -0,0 +1,23 @@
+{
+    "generate_vep_config": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                            "species": "homo_sapiens",
+                            "assembly": "GRCh38"
+                        },
+                        "homo_sapiens_GRCh38.ini:md5,d5a37bae4f24a697940c8d4efe9e7e0a"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2026-02-02T20:41:08.6921"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/prepare_genome.nf b/nextflow/vcf_prepper/subworkflows/local/prepare_genome.nf
deleted file mode 100755
index 18de3dfb..00000000
--- a/nextflow/vcf_prepper/subworkflows/local/prepare_genome.nf
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-//
-// Prepare genome related files
-//
-
-include { GENERATE_CHROM_SIZES } from "../../modules/local/generate_chrom_sizes.nf"
-include { GENERATE_VEP_CONFIG } from "../../modules/local/generate_vep_config.nf"
-include { GENERATE_SYNONYM_FILE } from "../../modules/local/generate_synonym_file.nf"
-include { PROCESS_CACHE } from "../../modules/local/process_cache.nf"
-include { PROCESS_GFF } from "../../modules/local/process_gff.nf"
-include { PROCESS_FASTA } from "../../modules/local/process_fasta.nf"
-include { PROCESS_CONSERVATION_DATA } from "../../modules/local/process_conservation_data.nf"
-include { PROCESS_INPUT } from "../../modules/local/process_input.nf"
-
-workflow PREPARE_GENOME {
-  take:
-    input
-  
-  main:
-    input
-    .map {
-      meta, vcf ->
-        genome_temp_dir = "${params.temp_dir}/${meta.genome_uuid}"
-        file(genome_temp_dir).mkdirs()
-        
-        synonym_file = "${genome_temp_dir}/${meta.genome}.synonyms"
-        vep_config = "${genome_temp_dir}/${meta.genome}.ini"
-        chrom_sizes = "${genome_temp_dir}/${meta.genome}.chrom.sizes"
-        
-        genome_api_outdir = "${params.output_dir}/api/${meta.genome_uuid}"
-        file(genome_api_outdir).mkdirs()
-        genome_tracks_outdir = "${params.output_dir}/tracks/${meta.genome_uuid}"
-        file(genome_tracks_outdir).mkdirs()
-        
-        cache_dir = params.cache_dir ? params.cache_dir : genome_temp_dir
-        gff_dir = params.gff_dir ? params.gff_dir : genome_temp_dir
-        fasta_dir = params.fasta_dir ? params.fasta_dir : genome_temp_dir
-        conservation_data_dir = params.conservation_data_dir ? params.conservation_data_dir : genome_temp_dir
-        
-        [ meta + [
-            synonym_file: synonym_file,
-            vep_config: vep_config,
-            chrom_sizes: chrom_sizes,
-            genome_temp_dir: genome_temp_dir,
-            genome_api_outdir: genome_api_outdir,
-            genome_tracks_outdir: genome_tracks_outdir,
-            cache_dir: cache_dir,
-            gff_dir: gff_dir,
-            fasta_dir: fasta_dir,
-            conservation_data_dir: conservation_data_dir
-          ], vcf
-        ]
-    }.set { ch_prepare_genome }
-
-    // post prepare steps only need meta
-    ch_prepare_genome
-    .map {
-      meta, vcf -> meta
-    }
-    .set { ch_prepare_genome_meta }
-
-    // if we skip we only need a channel with tag value
-    ch_prepare_genome_meta
-    .map { 
-      meta -> 
-        meta.genome 
-    }
-    .set { ch_skip }
-    
-    // TODO: run this only once per genome when we have multiple source (not DOWNLOAD_SOURCE)
-    // prepare for api files
-    if (!params.skip_vep) {
-      ch_synonym_file_done = GENERATE_SYNONYM_FILE( ch_prepare_genome_meta )
-    
-      if(params.use_vep_cache){
-        ch_processed_cache_or_gff = PROCESS_CACHE( ch_prepare_genome_meta )
-      }
-      else {
-        ch_processed_cache_or_gff = PROCESS_GFF( ch_prepare_genome_meta )
-      }
-      ch_processed_fasta = PROCESS_FASTA( ch_prepare_genome_meta )
-      ch_processed_conservation = PROCESS_CONSERVATION_DATA( ch_prepare_genome_meta )
-      
-      ch_prepare_genome_meta
-      .map {
-        meta -> 
-          [meta.genome, meta]
-      }
-      .join( ch_processed_cache_or_gff )
-      .join( ch_processed_fasta )
-      .join( ch_processed_conservation )
-      .map {
-        genome, meta ->
-          meta
-      }
-      .set { ch_generate_vep_config }
-      
-      ch_vep_config_done = GENERATE_VEP_CONFIG( ch_generate_vep_config )
-
-      ch_synonym_file_done
-      .join( ch_vep_config_done )
-      .set { ch_prepared_api }
-    }
-    else {
-      ch_prepared_api = ch_skip
-    }
-
-    // prepare for tracks files
-    ch_prepared_track = params.skip_tracks ? ch_skip : GENERATE_CHROM_SIZES( ch_prepare_genome_meta )
-
-    // we join channels to only create DAG edges
-    ch_prepare_genome
-    .map {
-      meta, vcf ->
-        // tag here is the genome
-        tag = meta.genome 
-        [tag, meta, vcf]
-    }
-    .join ( ch_prepared_api )
-    .join ( ch_prepared_track )
-    .map {
-      tag, meta, vcf ->
-        [meta, vcf]
-    }
-    .set { ch_prepare_source }
-    
-    PROCESS_INPUT( ch_prepare_source )
-    
-    emit:
-      PROCESS_INPUT.out
-}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/prepare_genome/main.nf b/nextflow/vcf_prepper/subworkflows/local/prepare_genome/main.nf
new file mode 100644
index 00000000..2dc90cf5
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/prepare_genome/main.nf
@@ -0,0 +1,56 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+ 
+//
+// Prepare genome related files
+//
+
+include { GENERATE_SYNONYM_FILE } from "../../../modules/local/generate_synonym_file"
+include { GENERATE_CHROM_SIZES } from "../../../modules/local/generate_chrom_sizes"
+
+workflow PREPARE_GENOME {
+    take:
+    genome_meta                 // channel: [ val(genome_meta) ]
+    version                     //     int: Ensembl (old) release version / schema version
+    ini_file                    //     str: INI file with database connection info
+  
+    main:
+    // create genome specific directories
+    genome_meta
+    .map {
+        meta ->
+            file(meta.genome_temp_dir).mkdirs()
+            file(meta.genome_api_outdir).mkdirs()
+            file(meta.genome_tracks_outdir).mkdirs()
+
+        meta
+    }.set { ch_prepare_genome }
+
+    GENERATE_SYNONYM_FILE( 
+        ch_prepare_genome,
+        version,
+        ini_file
+    )
+    GENERATE_CHROM_SIZES( 
+        ch_prepare_genome,
+        version,
+        ini_file 
+    )
+    
+    emit:
+    synonym_file = GENERATE_SYNONYM_FILE.out
+    chrom_sizes_file = GENERATE_CHROM_SIZES.out
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/prepare_genome/tests/main.nf.test b/nextflow/vcf_prepper/subworkflows/local/prepare_genome/tests/main.nf.test
new file mode 100644
index 00000000..16cfadae
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -0,0 +1,75 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_workflow {
+
+    name "Test workflow PREPARE_GENOME"
+    script "../main.nf"
+    workflow "PREPARE_GENOME"
+
+    test("prepare_genome") {
+
+        when {
+            workflow {
+                """
+                genome_meta = [
+                    [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                        'genome':'homo_sapiens_grch38', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_api_outdir':"${workDir}/path/to/output/api/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_tracks_outdir':"${workDir}/path/to/output/tracks/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'synonym_file':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.synonyms",
+                        'chrom_sizes_file':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.chrom.sizes",
+                    ]
+                ]
+
+                input[0] = Channel.fromList(genome_meta)
+                input[1] = 110
+                input[2] = "${projectDir}/tests/testdata/test_db.ini"
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+
+            // genome specific directories created
+            assert file("${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb").exists()
+            assert file("${workDir}/path/to/output/api/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb").exists()
+            assert file("${workDir}/path/to/output/tracks/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb").exists()
+
+            // genome_meta does not change
+            assert workflow.out.get(0).get(0).get(0) == [
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                        'genome':'homo_sapiens_grch38', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_api_outdir':"${workDir}/path/to/output/api/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_tracks_outdir':"${workDir}/path/to/output/tracks/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'synonym_file':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.synonyms",
+                        'chrom_sizes_file':"${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.chrom.sizes",
+                    ]
+
+            assert file("${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.synonyms").exists()
+            assert file("${workDir}/path/to/temp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.chrom.sizes").exists()
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep.nf b/nextflow/vcf_prepper/subworkflows/local/run_vep.nf
deleted file mode 100755
index 9f7b9e66..00000000
--- a/nextflow/vcf_prepper/subworkflows/local/run_vep.nf
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-//
-// run VEP annotation
-//
-
-repo_dir = params.repo_dir
-
-include { INDEX_VCF } from "../../modules/local/index_vcf.nf"
-include { vep } from "${repo_dir}/ensembl-vep/nextflow/workflows/run_vep.nf"
-
-workflow RUN_VEP {
-  take:
-    input
-  
-  main:
-  // create index file at the exact location where input vcf file is as nextflow-vep requires as such
-  input
-  .map {
-    meta, vcf ->
-      // vcf_fullpath = vcf.toString()
-      [meta, vcf]
-  }
-  .set { ch_index_vcf }
-  INDEX_VCF( ch_index_vcf )
-  
-  INDEX_VCF.out
-  .map {
-    meta, vcf, vcf_index ->
-      vep_meta = [:]
-      vep_meta.output_dir = meta.genome_temp_dir
-      vep_meta.one_to_many = 0
-      vep_meta.index_type = meta.index_type
-      vep_meta.filters = "amino_acids not match X[A-Za-z*]?\\/"
-
-      [meta: vep_meta, file: vcf, index: vcf_index, vep_config: meta.vep_config]
-  }
-  .set { ch_vep }
-  vep( ch_vep )
-  
-  input
-  .map {
-    meta, vcf ->
-      // tag here is the output vcf file from nextflow-vep
-      filename = file("${meta.genome}-${meta.source}.vcf.gz").getBaseName() + "_VEP.vcf.gz"
-      tag = "${meta.genome_temp_dir}/${filename}"
-
-      [tag, meta]
-  }
-  .join ( vep.out, failOnDuplicate: true )
-  .map {
-    tag, meta ->
-      vcf = tag
-      vcf_index = "${tag}.${meta.index_type}"
-
-      if (! file(vcf).exists() || ! file(vcf_index).exists()){
-        exit 1, "ERROR: Could not find nextflow-vep output files. Check the following - \n\tVCF - ${vcf}\n\tVCF index - ${vcf_index}"
-      }
-      
-      [meta, vcf, vcf_index]
-  }.set { ch_post_vep }
-  
-  emit:
-    ch_post_vep
-}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/main.nf b/nextflow/vcf_prepper/subworkflows/local/run_vep/main.nf
new file mode 100644
index 00000000..e30244eb
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/run_vep/main.nf
@@ -0,0 +1,65 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+repo_dir = params.repo_dir
+include { vep } from "${repo_dir}/ensembl-vep/nextflow/workflows/run_vep.nf"
+
+workflow RUN_VEP {
+    take:
+    ch_input                // channel: [ val(genome_meta), path(vcf), path(vcf_index), path(vep_config) ]
+
+    main:
+    ch_input
+    .map {
+        genome_meta, file_meta, vcf, vcf_index, vep_config ->
+
+        def vep_meta = [:]
+        vep_meta.output_dir = genome_meta.genome_temp_dir
+        vep_meta.one_to_many = 0
+        vep_meta.index_type = "csi"
+        vep_meta.filters = "amino_acids not match X[A-Za-z*]?\\/"
+
+        [meta: vep_meta, file: vcf, index: vcf_index, vep_config: vep_config]
+    }
+    .set { ch_vep }
+    vep( ch_vep )
+
+    // join nextflow-vep output with genome_meta
+    ch_input
+    .map {
+        genome_meta, file_meta, vcf, vcf_index, vep_config ->
+
+        // match with nextflow-vep output filename - set in FORMAT_VCF step
+        filename = vcf.baseName + "_VEP.vcf.gz"
+        vep_output_file = "${genome_meta.genome_temp_dir}/${filename}"
+
+        [vep_output_file, genome_meta, file_meta]
+    }
+    .join ( vep.out, failOnDuplicate: true )
+    .map {
+        vep_output_file, genome_meta, file_meta ->
+        index_file = "${vep_output_file}.csi"
+
+        if (! file(vep_output_file).exists() || ! file(index_file).exists()) {
+            exit 1, "ERROR: Could not find nextflow-vep output files. Check the following - \n\tVCF - ${vcf}\n\tVCF index - ${vcf_index}"
+        }
+      
+        [genome_meta, file_meta, vep_output_file, index_file]
+    }.set { ch_post_vep }
+  
+    emit:
+    ch_post_vep
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test
new file mode 100644
index 00000000..88263d32
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test
@@ -0,0 +1,68 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_workflow {
+
+    name "Test subworkflow RUN_VEP"
+    script "../main.nf"
+    workflow "RUN_VEP"
+
+    test("run_vep") {
+
+        when {
+            workflow {
+                """
+                // use moduleDir for consistent snapshot
+                tmp_dir = "${moduleDir}/tests/temp"
+                file(tmp_dir).mkdirs()
+
+                genome_meta = [
+                        'genome':'homo_sapiens_grch38',
+                        'genome_temp_dir':tmp_dir
+                    ]
+				file_meta = [:]
+                vcf = file("${moduleDir}/tests/testdata/test.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf.gz.csi")
+                vep_config = file("${moduleDir}/tests/testdata/test_vep_config.ini")
+
+                input[0] = Channel.of([genome_meta, file_meta, vcf, vcf_index, vep_config])
+                """
+            }
+        }
+
+        then {
+            // Do not check snapshot - it will change every time because of timestamp in header
+            assert workflow.success
+
+			// genome_meta does not change
+			def tmp_dir = "${moduleDir}/tests/temp"
+			assert workflow.out.get(0).get(0).get(0) == [
+                        'genome':'homo_sapiens_grch38',
+                        'genome_temp_dir':tmp_dir
+                    ]
+			
+			// file name ok
+			assert workflow.out.get(0).get(0).get(2) == tmp_dir + "/test.vcf_VEP.vcf.gz"
+			assert workflow.out.get(0).get(0).get(3) == tmp_dir + "/test.vcf_VEP.vcf.gz.csi"
+
+			// file content ok
+            assert path(workflow.out.get(0).get(0).get(2)).linesGzip.size() == 11
+            assert path(workflow.out.get(0).get(0).get(2)).vcf.variants.size() == 1
+			def variant_line = path(workflow.out.get(0).get(0).get(2)).linesGzip[-1]
+			assert variant_line.equals("1\t230710048\trs699\tA\tG\t.\t.\tCSQ=G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000366667.6|protein_coding|2/5||||843|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000355627|genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000679684.1|protein_coding|2/5||||1287|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505981|genes.gff3.gz|||,G|missense_variant&NMD_transcript_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000679738.1|nonsense_mediated_decay|2/7||||1366|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505063|genes.gff3.gz|||,G|missense_variant&NMD_transcript_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000679802.1|nonsense_mediated_decay|2/8||||1287|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505184|genes.gff3.gz|||,G|non_coding_transcript_exon_variant|MODIFIER|AGT|ENSG00000135744|Transcript|ENST00000679854.1|retained_intron|2/6||||1287|||||||-1||SNV|1:230710047:A:G||||genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000679957.1|protein_coding|2/5||||1287|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000506646|genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000680041.1|protein_coding|2/5||||991|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000504866|genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000680783.1|protein_coding|2/3||||1287|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000506329|genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000681269.1|protein_coding|2/5||||868|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505985|genes.gff3.gz|||,G|non_coding_transcript_exon_variant|MODIFIER|AGT|ENSG00000135744|Transcript|ENST00000681347.1|retained_intron|2/6||||1287|||||||-1||SNV|1:230710047:A:G||||genes.gff3.gz|||,G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000681514.1|protein_coding|3/6||||930|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505963|genes.gff3.gz|||,G|missense_variant&NMD_transcript_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000681772.1|nonsense_mediated_decay|2/7||||1287|776|259|M/T|aTg/aCg|||-1||SNV|1:230710047:A:G|||ENSP00000505829|genes.gff3.gz|||")        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test.snap b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test.snap
new file mode 100644
index 00000000..00c53e77
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "run_vep": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "genome": "homo_sapiens_grch38",
+                            "genome_temp_dir": [
+                                "test.vcf_VEP.vcf.gz:md5,0e5951b8002be47066441465b90526de",
+                                "test.vcf_VEP.vcf.gz.csi:md5,977b2190a8bca5775d19979f662c4209"
+                            ]
+                        },
+                        "test.vcf_VEP.vcf.gz:md5,0e5951b8002be47066441465b90526de",
+                        "test.vcf_VEP.vcf.gz.csi:md5,977b2190a8bca5775d19979f662c4209"
+                    ]
+                ],
+                "ch_post_vep": [
+                    [
+                        {
+                            "genome": "homo_sapiens_grch38",
+                            "genome_temp_dir": [
+                                "test.vcf_VEP.vcf.gz:md5,0e5951b8002be47066441465b90526de",
+                                "test.vcf_VEP.vcf.gz.csi:md5,977b2190a8bca5775d19979f662c4209"
+                            ]
+                        },
+                        "test.vcf_VEP.vcf.gz:md5,0e5951b8002be47066441465b90526de",
+                        "test.vcf_VEP.vcf.gz.csi:md5,977b2190a8bca5775d19979f662c4209"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-10-17T21:54:08.522858"
+    },
+    "run workflow": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "file_type": "local",
+                            "source": "dbSNP",
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950",
+                            "sources_meta_file": "sources_meta.json:md5,2a825f7bdb1b8d158094073c7b6a7286",
+                            "index_type": "tbi"
+                        },
+                        "FORMATTED_test.vcf.gz:md5,c79a04c23606627b7b6d840b869026ae"
+                    ]
+                ],
+                "files": [
+                    [
+                        {
+                            "file_type": "local",
+                            "source": "dbSNP",
+                            "synonym_file": "homo_sapiens_grch38.synonyms:md5,4d2076f947bfda03b7644988ae595950",
+                            "sources_meta_file": "sources_meta.json:md5,2a825f7bdb1b8d158094073c7b6a7286",
+                            "index_type": "tbi"
+                        },
+                        "FORMATTED_test.vcf.gz:md5,c79a04c23606627b7b6d840b869026ae"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2025-09-09T15:04:48.226156"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz
new file mode 100644
index 00000000..9dd95455
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz.tbi b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz.tbi
new file mode 100644
index 00000000..7873b1ff
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz.tbi differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz
new file mode 100755
index 00000000..565bfca6
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..48392c5e
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test_vep_config.ini b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test_vep_config.ini
new file mode 100644
index 00000000..0197d615
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/test_vep_config.ini
@@ -0,0 +1,11 @@
+force_overwrite	1
+fork	2
+vcf	1
+spdi	1
+variant_class	1
+protein	1
+transcript_version	1
+gencode_promoter	1
+fasta	${BASE_DIR}/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz
+gff	${BASE_DIR}/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/genes.gff3.gz
+plugin Downstream
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz
new file mode 100644
index 00000000..a7eb692e
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.fai b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.fai
new file mode 100644
index 00000000..a2ce51ef
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.fai
@@ -0,0 +1 @@
+1	248956422	46	60	61
diff --git a/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.gzi b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.gzi
new file mode 100644
index 00000000..e4c33b8e
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/run_vep/tests/testdata/unmasked.fa.gz.gzi differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/split_vcf.nf b/nextflow/vcf_prepper/subworkflows/local/split_vcf/main.nf
similarity index 68%
rename from nextflow/vcf_prepper/subworkflows/local/split_vcf.nf
rename to nextflow/vcf_prepper/subworkflows/local/split_vcf/main.nf
index 19a9d462..5a0a8cbc 100755
--- a/nextflow/vcf_prepper/subworkflows/local/split_vcf.nf
+++ b/nextflow/vcf_prepper/subworkflows/local/split_vcf/main.nf
@@ -13,22 +13,22 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
- 
+
 //
 // Split large VCF
 //
 
-include { READ_VCF_CHR } from "../../modules/local/read_vcf_chr.nf"
-include { SPLIT_VCF_CHR } from "../../modules/local/split_vcf_chr.nf"
+include { READ_VCF_CHR } from "../../../modules/local/read_vcf_chr"
+include { SPLIT_VCF_CHR } from "../../../modules/local/split_vcf_chr"
 
 workflow SPLIT_VCF {
-  take:
-    input
-  
-  main:
-    READ_VCF_CHR( input )
-    SPLIT_VCF_CHR(READ_VCF_CHR.out.transpose())
+	take:
+	ch_input				// channel: [ val(genome_meta), path(vcf), path(vcf_index) ]
+
+	main:
+	READ_VCF_CHR(ch_input)
+	SPLIT_VCF_CHR(READ_VCF_CHR.out.transpose())
 
-  emit:
-    SPLIT_VCF_CHR.out
-}
\ No newline at end of file
+	emit:
+	SPLIT_VCF_CHR.out
+}
diff --git a/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/main.nf.test b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/main.nf.test
new file mode 100644
index 00000000..2ad63040
--- /dev/null
+++ b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/main.nf.test
@@ -0,0 +1,47 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_workflow {
+
+    name "Test workflow SPLIT_VCF"
+    script "../main.nf"
+    workflow "SPLIT_VCF"
+
+	test("split_vcf") {
+
+        when {
+            workflow {
+                """                
+                vcf = file("${moduleDir}/tests/testdata/test.vcf.gz")
+                vcf_index = file("${moduleDir}/tests/testdata/test.vcf.gz.csi")
+
+                input[0] = tuple([:], [:], vcf, vcf_index)
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+
+			// can we assume channel spitting fixed data here?
+            assert file(workflow.out.get(0).get(0).get(2)).name == "split.1.vcf.gz"
+            assert path(workflow.out.get(0).get(0).get(2)).vcf.chromosomes == ['1'] as Set
+            assert file(workflow.out.get(0).get(1).get(2)).name == "split.8.vcf.gz"
+            assert path(workflow.out.get(0).get(1).get(2)).vcf.chromosomes == ['8'] as Set
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz
new file mode 100644
index 00000000..5f498d9a
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz differ
diff --git a/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..e206e6b1
Binary files /dev/null and b/nextflow/vcf_prepper/subworkflows/local/split_vcf/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/tests/data/homo_sapiens_GRCh38.ini b/nextflow/vcf_prepper/tests/data/homo_sapiens_GRCh38.ini
deleted file mode 100755
index e3b81874..00000000
--- a/nextflow/vcf_prepper/tests/data/homo_sapiens_GRCh38.ini
+++ /dev/null
@@ -1,73 +0,0 @@
-force_overwrite 1
-fork 2
-species homo_sapiens
-assembly GRCh38
-cache_version 110
-cache /nfs/production/flicek/ensembl/variation/data/VEP/tabixconverted
-fasta /nfs/production/flicek/ensembl/variation/data/VEP/fasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
-offline 1
-vcf 1
-spdi 1
-regulatory 1
-pubmed 1
-var_synonyms 1
-variant_class 1
-sift b
-polyphen b
-af_1kg 1
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.1.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.2.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.3.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.4.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.5.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v2.1.1/grch38/exomes/gnomad.exomes.r2.1.1.sites.6.liftover_grch38_no_VEP.vcf.gz,short_name=gnomAD_exomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
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-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr16_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr17_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr18_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr19_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr20_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr21_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chr22_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chrX_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-custom file=/nfs/production/flicek/ensembl/variation/data/gnomAD/v3.1.2/grch38/genomes/gnomad.genomes.v3.1.2.sites.chrY_trimmed_info.vcf.bgz,short_name=gnomAD_genomes,format=vcf,type=exact,coords=0,fields=AF%AC%AN%AF_afr%AC_afr%AN_afr%AF_amr%AC_amr%AN_amr%AF_asj%AC_asj%AN_asj%AF_eas%AC_eas%AN_eas%AF_fin%AC_fin%AN_fin%AF_nfe%AC_nfe%AN_nfe%AF_oth%AC_oth%AN_oth%AF_sas%AC_sas%AN_sas
-dir_plugins /hps/software/users/ensembl/repositories/snhossain/VEP_plugins
-plugin CADD,/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/CADD_GRCh38_1.6_whole_genome_SNVs.tsv.gz,/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/CADD_GRCh38_1.6_InDels.tsv.gz
-plugin REVEL,/nfs/production/flicek/ensembl/variation/data/REVEL/2021-may/new_tabbed_revel_grch38.tsv.gz
-plugin SpliceAI,snv=/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/spliceai_scores.masked.snv.hg38.vcf.gz,indel=/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/spliceai_scores.masked.indel.hg38.vcf.gz
-plugin Phenotypes,file=/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/Phenotypes_data_files/Phenotypes.pm_homo_sapiens_110_GRCh38.gvf.gz,phenotype_feature=1
-plugin IntAct,mutation_file=/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/mutations.tsv,mapping_file=/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/mutation_gc_map.txt.gz,pmid=1
-plugin AncestralAllele,/nfs/production/flicek/ensembl/variation/enseweb-data_tools/grch38/e110/vep/plugin_data/homo_sapiens_ancestor_GRCh38_109.fa.gz
-plugin Conservation,/nfs/production/flicek/ensembl/variation/data/Conservation/gerp_conservation_scores.homo_sapiens.GRCh38.bw
diff --git a/nextflow/vcf_prepper/tests/data/test_runvep.vcf.gz.tbi b/nextflow/vcf_prepper/tests/data/test_runvep.vcf.gz.tbi
deleted file mode 100755
index de08630c..00000000
Binary files a/nextflow/vcf_prepper/tests/data/test_runvep.vcf.gz.tbi and /dev/null differ
diff --git a/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz b/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz
deleted file mode 100755
index 0474f0ce..00000000
Binary files a/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz and /dev/null differ
diff --git a/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz.tbi b/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz.tbi
deleted file mode 100755
index ec157027..00000000
Binary files a/nextflow/vcf_prepper/tests/data/test_updatefields.vcf.gz.tbi and /dev/null differ
diff --git a/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz b/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz
deleted file mode 100755
index e5d89b7e..00000000
Binary files a/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz and /dev/null differ
diff --git a/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz.tbi b/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz.tbi
deleted file mode 100755
index d56fa776..00000000
Binary files a/nextflow/vcf_prepper/tests/data/test_vcftobed.vcf.gz.tbi and /dev/null differ
diff --git a/nextflow/vcf_prepper/tests/main.functions.nf.test b/nextflow/vcf_prepper/tests/main.functions.nf.test
new file mode 100644
index 00000000..aec3258c
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/main.functions.nf.test
@@ -0,0 +1,255 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_function {
+
+    name "Test functions"
+    script "../main.nf"
+
+    test("function - initialise") {
+
+        function "initialise"
+
+        when {
+            params {
+                output_dir = "path/to/output"
+                temp_dir = "path/to/temp"
+            }
+            function {
+                """
+                input[0] = params
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert file(workDir + "/../" + params.output_dir + "/api").exists()
+            assert file(workDir + "/../" + params.output_dir + "/tracks").exists()
+        }
+    }
+
+	test("function - process_vep_config") {
+
+        function "process_vep_config"
+
+        when {
+            params {
+                vep_config = "${projectDir}/tests/testdata/vep_config.json"
+                skip_vep = 0
+            }
+            function {
+                """
+                input[0] = params
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result == [
+				'annotation_source':[
+					'gff':[
+						'active':true
+					], 
+					'fasta':[
+						'active':true
+					], 
+					'cache':[
+						'active':false
+					]
+				], 
+				'default_options':[
+					'force_overwrite':1, 
+					'fork':1, 
+					'vcf':1, 
+					'spdi':1, 
+					'variant_class':1, 
+					'protein':1, 
+					'transcript_version':1, 
+					'gencode_promoter':1
+				], 
+				'plugins':[
+                    'conf':[
+                        [
+                            'name':'CADD', 
+                            'keyed':true
+                        ],
+                        [
+                            'name':'SpliceAI', 
+                            'keyed':true
+                        ]
+                    ]
+                ], 
+				'custom_annotaions':[
+                    'conf':[]
+                ]
+			]
+        }
+    }
+
+    test("function - process_vep_config - missing confs") {
+
+        function "process_vep_config"
+
+        when {
+            params {
+                vep_config = "${projectDir}/tests/testdata/vep_config_missing_confs.json"
+                skip_vep = 0
+            }
+            function {
+                """
+                input[0] = params
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result == [
+				'annotation_source':[
+					'gff':[
+						'active':true
+					], 
+					'fasta':[
+						'active':true
+					], 
+					'cache':[
+						'active':false
+					]
+				], 
+				'default_options':[
+					'force_overwrite':1, 
+					'fork':1, 
+					'vcf':1, 
+					'spdi':1, 
+					'variant_class':1, 
+					'protein':1, 
+					'transcript_version':1, 
+					'gencode_promoter':1
+				], 
+				'plugins':[:], 
+				'custom_annotaions':[:]
+			]
+        }
+    }
+
+    test("function - genome_map_from_input_config") {
+
+        function "genome_map_from_input_config"
+
+        when {
+            params {
+                output_dir = "${projectDir}"
+                temp_dir = "${projectDir}/tmp"
+            }
+            function {
+                """
+                def example_input_config = "${moduleDir}/assets/examples/example_input_config.json"
+                def input_config = new groovy.json.JsonSlurper().parse(file(example_input_config))
+
+                input[0] = input_config
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result == [
+                    '2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb':[
+                        'genome_uuid':'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb',
+                        'genome':'homo_sapiens_grch38', 
+                        'species':'homo_sapiens', 
+                        'assembly':'GRCh38',
+                        'genome_temp_dir':"${projectDir}/tmp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_api_outdir':"${projectDir}/api/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'genome_tracks_outdir':"${projectDir}/tracks/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                        'synonym_file':"${projectDir}/tmp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.synonyms",
+                        'chrom_sizes_file':"${projectDir}/tmp/2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb/homo_sapiens_grch38.chrom.sizes"
+                    ], 
+                    '3704ceb1-948d-11ec-a39d-005056b38ce3':[
+                        'genome_uuid':'3704ceb1-948d-11ec-a39d-005056b38ce3',
+                        'genome':'homo_sapiens_grch37', 
+                        'species':'homo_sapiens_37', 
+                        'assembly':'GRCh37',
+                        'genome_temp_dir':"${projectDir}/tmp/3704ceb1-948d-11ec-a39d-005056b38ce3",
+                        'genome_api_outdir':"${projectDir}/api/3704ceb1-948d-11ec-a39d-005056b38ce3",
+                        'genome_tracks_outdir':"${projectDir}/tracks/3704ceb1-948d-11ec-a39d-005056b38ce3",
+                        'synonym_file':"${projectDir}/tmp/3704ceb1-948d-11ec-a39d-005056b38ce3/homo_sapiens_grch37.synonyms",
+                        'chrom_sizes_file':"${projectDir}/tmp/3704ceb1-948d-11ec-a39d-005056b38ce3/homo_sapiens_grch37.chrom.sizes"
+                    ], 
+                    'a73357ab-93e7-11ec-a39d-005056b38ce3':[
+                        'genome_uuid':'a73357ab-93e7-11ec-a39d-005056b38ce3',
+                        'genome':'triticum_aestivum_IWGSC', 
+                        'species':'triticum_aestivum', 
+                        'assembly':'IWGSC',
+                        'genome_temp_dir':"${projectDir}/tmp/a73357ab-93e7-11ec-a39d-005056b38ce3",
+                        'genome_api_outdir':"${projectDir}/api/a73357ab-93e7-11ec-a39d-005056b38ce3",
+                        'genome_tracks_outdir':"${projectDir}/tracks/a73357ab-93e7-11ec-a39d-005056b38ce3",
+                        'synonym_file':"${projectDir}/tmp/a73357ab-93e7-11ec-a39d-005056b38ce3/triticum_aestivum_IWGSC.synonyms",
+                        'chrom_sizes_file':"${projectDir}/tmp/a73357ab-93e7-11ec-a39d-005056b38ce3/triticum_aestivum_IWGSC.chrom.sizes"
+                    ]
+                ]
+        }
+    }
+
+    test("function - get_vcf_channel_list") {
+
+        function "get_vcf_channel_list"
+
+        when {
+            function {
+                """
+                def example_input_config = "${moduleDir}/assets/examples/example_input_config.json"
+                def input_config = new groovy.json.JsonSlurper().parse(file(example_input_config))
+                def genome_map = [
+                    '2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb':
+                        ['genome':'homo_sapiens_grch38', 'species':'homo_sapiens', 'assembly':'GRCh38'], 
+                    '3704ceb1-948d-11ec-a39d-005056b38ce3':
+                        ['genome':'homo_sapiens_grch37', 'species':'homo_sapiens_37', 'assembly':'GRCh37'], 
+                    'a73357ab-93e7-11ec-a39d-005056b38ce3':
+                        ['genome':'triticum_aestivum_IWGSC', 'species':'triticum_aestivum', 'assembly':'IWGSC']
+                    ]
+
+                input[0] = input_config
+                input[1] = genome_map
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result == [
+                [
+                    ['genome':'homo_sapiens_grch38', 'species':'homo_sapiens', 'assembly':'GRCh38'], 
+                    ['source':'dbSNP', 'file_type':'local', 'multiple_source':false], 
+                    '/nfs/production/flicek/ensembl/variation/data/dbSNP/latest/GCF_000001405.40.gz'
+                ], 
+                [
+                    ['genome':'homo_sapiens_grch37', 'species':'homo_sapiens_37', 'assembly':'GRCh37'], 
+                    ['source':'dbSNP', 'file_type':'local', 'multiple_source':false], 
+                    '/nfs/production/flicek/ensembl/variation/data/dbSNP/latest/GCF_000001405.25.gz'
+                ],
+                [
+                    ['genome':'triticum_aestivum_IWGSC', 'species':'triticum_aestivum', 'assembly':'IWGSC'],
+                    ['source':'MULTIPLE', 'file_type':'remote', 'multiple_source':false, 'sources':'[CerealsDB,%20EMS-induced%20mutation,%20Inter-homoeologous,%20Nottingham_WRC,%20Watkins-exome-capture,%20Exome_Capture_Diversity,%20Watkins_collection]'], 
+                    'https://ftp.ebi.ac.uk/ensemblgenomes/pub/release-57/plants/variation/vcf/triticum_aestivum/triticum_aestivum.vcf.gz'
+                ]
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/main.nf.test b/nextflow/vcf_prepper/tests/main.nf.test
new file mode 100644
index 00000000..1e849abe
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/main.nf.test
@@ -0,0 +1,85 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+nextflow_pipeline {
+
+    name "Test workflow VCF_PREPPER"
+    script "../main.nf"
+    tag "pipeline"
+
+    test("skips - all") {
+
+        when {
+            params {
+				input_config = "${projectDir}/tests/testdata/input_config.json"
+				vep_config = "${projectDir}/tests/testdata/vep_config.json"
+				ini_file = "${projectDir}/tests/testdata/test_db.ini"
+                skip_vep = 1
+                skip_tracks = 1
+                skip_stats = 1
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stdout.contains("Nothing to do...")
+        }
+    }
+
+    test("skips - none") {
+
+        when {
+            params {
+                // create temp dir for output
+                tmp_dir = "${projectDir}/temp"
+                file(tmp_dir).mkdirs()
+
+				output_dir = tmp_dir
+				input_config = "${projectDir}/tests/testdata/input_config.json"
+				vep_config = "${projectDir}/tests/testdata/vep_config.json"
+				ini_file = "${projectDir}/tests/testdata/test_db.ini"
+                bin_size = 10
+                version = 110
+            }
+        }
+
+        then {
+            assert workflow.success // unexpected: summary_stats missing gnomAD_genomes_AF [fixed @dev_v1.0]
+        }
+    }
+
+    test("vep_config - missing confs") {
+
+        when {
+            params {
+                // create temp dir for output
+                tmp_dir = "${projectDir}/temp"
+                file(tmp_dir).mkdirs()
+
+				output_dir = tmp_dir
+				input_config = "${projectDir}/tests/testdata/input_config.json"
+				vep_config = "${projectDir}/tests/testdata/vep_config_missing_confs.json"
+				ini_file = "${projectDir}/tests/testdata/test_db.ini"
+                bin_size = 10
+            }
+        }
+
+        then {
+            assert workflow.success // unexpected: summary_stats missing gnomAD_genomes_AF [fixed @dev_v1.0]
+        }
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/modules/local/remove_variants.nf.test b/nextflow/vcf_prepper/tests/modules/local/remove_variants.nf.test
deleted file mode 100755
index 7924d204..00000000
--- a/nextflow/vcf_prepper/tests/modules/local/remove_variants.nf.test
+++ /dev/null
@@ -1,105 +0,0 @@
-nextflow_process {
-
-    name "Test Process REMOVE_VARIANTS"
-    script "modules/local/remove_variants.nf"
-    process "REMOVE_VARIANTS"
-
-    test("Default - remove both") {
-
-        when {
-            params {
-                remove_nonunique_ids = 1
-                remove_patch_regions = 1
-            }
-            process {
-                """
-                input[0] = tuple("NONE", file("$baseDir/tests/data/test_removevariants.vcf.gz"))
-                """
-            }
-        }
-
-        then {
-            // assert process run correctly
-            assert process.success
-            
-            // assert the content of the output file - no variants, only header lines
-            assert path(process.out.get(0).get(0).get(1)).linesGzip.size() == 5
-        }
-
-    }
-    
-    test("Only remove patch regions") {
-
-        when {
-            params {
-                remove_nonunique_ids = 0
-                remove_patch_regions = 1
-            }
-            process {
-                """
-                input[0] = tuple("NONE", file("$baseDir/tests/data/test_removevariants.vcf.gz"))
-                """
-            }
-        }
-
-        then {
-            // assert process run correctly
-            assert process.success
-
-            // assert the content of the output file - one variant
-            assert path(process.out.get(0).get(0).get(1)).linesGzip.size() == 6
-
-        }
-
-    }
-    
-    test("Only remove non-unique ids") {
-
-        when {
-            params {
-                remove_nonunique_ids = 1
-                remove_patch_regions = 0
-            }
-            process {
-                """
-                input[0] = tuple("NONE", file("$baseDir/tests/data/test_removevariants.vcf.gz"))
-                """
-            }
-        }
-
-        then {
-            // assert process run correctly
-            assert process.success
-            
-            // assert the content of the output file - one variant
-            assert path(process.out.get(0).get(0).get(1)).linesGzip.size() == 6
-            
-        }
-
-    }
-    
-    test("Remove none") {
-
-        when {
-            params {
-                remove_nonunique_ids = 0
-                remove_patch_regions = 0
-            }
-            process {
-                """
-                input[0] = tuple("NONE", file("$baseDir/tests/data/test_removevariants.vcf.gz"))
-                """
-            }
-        }
-
-        then {
-            // assert process run correctly
-            assert process.success
-            
-            // assert the content of the output file - three variants
-            assert path(process.out.get(0).get(0).get(1)).linesGzip.size() == 8
-        }
-
-    }
-
-}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/modules/local/update_fields.nf.test b/nextflow/vcf_prepper/tests/modules/local/update_fields.nf.test
deleted file mode 100755
index fac2e83b..00000000
--- a/nextflow/vcf_prepper/tests/modules/local/update_fields.nf.test
+++ /dev/null
@@ -1,88 +0,0 @@
-nextflow_process {
-
-    name "Test Process UPDATE_FIELDS"
-    script "modules/local/update_fields.nf"
-    process "UPDATE_FIELDS"
-
-    test("Source not clinvar") {
-
-        when {
-            params {
-                rename_clinvar_ids = 1
-            }
-            process {
-                """
-                input[0] = Channel.of(
-                    [
-                        [
-                            source: "test_source",
-                            synonym_file: "$baseDir/tests/data/homo_sapiens_grch38.synonyms"
-                        ], 
-                        "$baseDir/tests/data/test_updatefields.vcf.gz",
-                        "$baseDir/tests/data/test_updatefields.vcf.gz.tbi"
-                    ]
-                )
-                """
-            }
-        }
-
-        then {
-            assert process.success
-
-            def output_file = file(process.out.get(0).get(0).get(1))
-            def lines = output_file.readLines()
-            assert lines.size() == 7
-
-            assert lines[0].equals("##fileformat=VCFv4.2")
-            assert lines[1].equals("##INFO=<ID=SOURCE,Number=1,Type=String,Description=\"Source of the variation data\">")
-            assert lines[2].equals("##contig=<ID=1>")
-            assert lines[3].equals("##contig=<ID=Y>")
-            assert lines[4].equals("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO")
-            assert lines[5].equals("1\t925952\t1019397\tG\tA\t.\t.\tSOURCE=test_source")
-            assert lines[6].equals("Y\t2787033\t652674\tAG\tA\t.\t.\tSOURCE=test_source")
-        }
-
-    }
-
-    test("Source clinvar") {
-
-        when {
-            params {
-                rename_clinvar_ids = 1
-            }
-            process {
-                """
-                input[0] = Channel.of(
-                    [
-                        [
-                            source: "ClinVar",
-                            synonym_file: "$baseDir/tests/data/homo_sapiens_grch38.synonyms"
-                        ], 
-                        "$baseDir/tests/data/test_updatefields.vcf.gz",
-                        "$baseDir/tests/data/test_updatefields.vcf.gz.tbi"
-                    ]
-                )
-                """
-            }
-        }
-
-        then {
-            assert process.success
-
-            def output_file = file(process.out.get(0).get(0).get(1))
-            def lines = output_file.readLines()
-            assert lines.size() == 7
-
-            assert lines[0].equals("##fileformat=VCFv4.2")
-            assert lines[1].equals("##INFO=<ID=SOURCE,Number=1,Type=String,Description=\"Source of the variation data\">")
-            assert lines[2].equals("##contig=<ID=1>")
-            assert lines[3].equals("##contig=<ID=Y>")
-            assert lines[4].equals("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO")
-            assert lines[5].equals("1\t925952\tVCV001019397\tG\tA\t.\t.\tSOURCE=ClinVar")
-            assert lines[6].equals("Y\t2787033\tVCV000652674\tAG\tA\t.\t.\tSOURCE=ClinVar")
-        }
-
-    }
-
-
-}
diff --git a/nextflow/vcf_prepper/tests/nextflow.config b/nextflow/vcf_prepper/tests/nextflow.config
index c19b1ad0..ccc4759b 100755
--- a/nextflow/vcf_prepper/tests/nextflow.config
+++ b/nextflow/vcf_prepper/tests/nextflow.config
@@ -1,5 +1,40 @@
-/*
-========================================================================================
-    Nextflow config file for running tests
-========================================================================================
-*/
+singularity.enabled = false
+        
+process{
+	withName: SPLIT_VCF_CHR {
+        memory = 50.MB
+    }
+
+    withName: SPLIT_VCF_CHR {
+        memory = 10.MB
+    }
+
+    withName: runVEPonVCF {
+        cpus = 1
+        memory = 200.MB
+    }
+}
+
+profiles {
+    github {
+        docker{
+            enabled = true
+            runOptions = '-u $(id -u):$(id -g)'
+        }
+
+        params.repo_dir = "${projectDir}/repos"
+       
+        process{        
+            withLabel: bcftools {
+                container = null
+            }
+ 
+            withLabel: vep {
+                container = 'ensemblorg/ensembl-vep'
+            }
+        }
+    }
+    local {
+        params.repo_dir = "/Users/snhossain/ensembl-repos"
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/subworkflows/local/run_vep.nf.test b/nextflow/vcf_prepper/tests/subworkflows/local/run_vep.nf.test
deleted file mode 100755
index 72c72215..00000000
--- a/nextflow/vcf_prepper/tests/subworkflows/local/run_vep.nf.test
+++ /dev/null
@@ -1,100 +0,0 @@
-nextflow_workflow {
-
-    name "Test Workflow RUN_VEP"
-    script "subworkflows/local/run_vep.nf"
-    workflow "RUN_VEP"
-
-    test("Should run without failures") {
-
-        when {
-            workflow {
-                """
-                input[0] = Channel.of(
-                    [
-                        [
-                            genome_api_outdir: "$workDir", 
-                            index_type: "tbi",
-                            genome: "test_genome",
-                            source: "test_source",
-                            vep_config: "$baseDir/tests/data/homo_sapiens_GRCh38.ini"
-                        ], 
-                        "$baseDir/tests/data/test_runvep.vcf.gz"
-                    ]
-                )
-                """
-            }
-        }
-
-        then {
-            assert workflow.success
-            with (workflow.out.ch_post_vep) {
-                assert size() == 1
-                
-                assert get(0).get(1) ==~ ".*/test_genome-test_source_VEP.vcf.gz" 
-                path(get(0).get(1)).linesGzip.size() == 82
-                
-                def line = path(get(0).get(1)).linesGzip[81]
-                def consequences = line
-                    .split("\t")[7]
-                    .split("CSQ=")[-1]
-                    .split(",")[0]
-                    .split("\\|")
-
-                // Allele
-                assert consequences[0].equals("G")
-                // Consequence
-                assert consequences[1].equals("missense_variant")
-                // Feature
-                assert consequences[6].equals("ENST00000366667")
-                // Existing variant
-                assert consequences[17].equals("rs699&CM920010&COSV64184214")
-                // Variant class
-                assert consequences[21].equals("SNV")
-                // SPDI
-                assert consequences[22].equals("1:230710047:A:G")
-                // SIFT
-                assert consequences[26].equals("tolerated(1)")
-                // PolyPhen
-                assert consequences[27].equals("benign(0)")
-                // 1kg AF
-                assert consequences[28].equals("0.7051")
-                assert consequences[29].equals("0.9032")
-                assert consequences[30].equals("0.6354")
-                assert consequences[31].equals("0.8532")
-                assert consequences[32].equals("0.4115")
-                assert consequences[33].equals("0.636")
-                // Pubmed
-                assert consequences[37].contains("21533139")
-                // Variant synonyms
-                assert consequences[38].contains("UniProt::VAR_007096")
-                assert consequences[38].contains("COSMIC::COSM425562")
-                assert consequences[38].contains("PharmGKB::PA166153539")
-                // CADD
-                assert consequences[44].equals("0.347")
-                assert consequences[45].equals("-0.277922")
-                // REVEL
-                assert consequences[46].equals("0.157")
-                // SpliceAI
-                assert consequences[47].equals("-19")
-                assert consequences[48].equals("34")
-                assert consequences[49].equals("-47")
-                assert consequences[50].equals("45")
-                assert consequences[51].equals("0.00")
-                assert consequences[52].equals("0.00")
-                assert consequences[53].equals("0.00")
-                assert consequences[54].equals("0.00")
-                assert consequences[55].equals("AGT")
-                // Phenotypes
-                assert consequences[56].contains("HYPERTENSION__ESSENTIAL__SUSCEPTIBILITY_TO+ClinVar+rs699")
-                // Ancestral Allele
-                assert consequences[60].equals("G")
-                // GERP
-                assert consequences[61].equals("-2.920")
-                // gnomAD AF
-                assert consequences[62..117].join("").size() > 56
-            }
-        }
-
-    }
-
-}
diff --git a/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz b/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz
new file mode 100644
index 00000000..5700a622
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz differ
diff --git a/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz b/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz
new file mode 100644
index 00000000..1360ba65
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz differ
diff --git a/nextflow/vcf_prepper/tests/testdata/ensembl_genome_metadata.dump b/nextflow/vcf_prepper/tests/testdata/ensembl_genome_metadata.dump
new file mode 100644
index 00000000..43a37632
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/ensembl_genome_metadata.dump
@@ -0,0 +1,472 @@
+-- MySQL dump 10.13  Distrib 5.7.44, for Linux (x86_64)
+--
+-- Database: ensembl_genome_metadata
+-- ------------------------------------------------------
+-- Server version	5.6.36-log
+
+/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
+/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
+/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
+/*!40101 SET NAMES utf8 */;
+/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
+/*!40103 SET TIME_ZONE='+00:00' */;
+/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
+/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
+/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
+/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
+
+--
+-- Table structure for table `assembly`
+--
+
+DROP TABLE IF EXISTS `assembly`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `assembly` (
+  `assembly_id` int(11) NOT NULL AUTO_INCREMENT,
+  `ucsc_name` varchar(16) DEFAULT NULL,
+  `accession` varchar(16) NOT NULL,
+  `level` varchar(32) NOT NULL,
+  `name` varchar(128) NOT NULL,
+  `accession_body` varchar(32) DEFAULT NULL,
+  `assembly_default` varchar(128) DEFAULT NULL,
+  `tol_id` varchar(32) DEFAULT NULL,
+  `created` datetime(6) DEFAULT NULL,
+  `ensembl_name` varchar(255) DEFAULT NULL,
+  `alt_accession` varchar(16) DEFAULT NULL,
+  `assembly_uuid` char(40) NOT NULL,
+  `is_reference` tinyint(1) NOT NULL,
+  `url_name` varchar(128) DEFAULT NULL,
+  PRIMARY KEY (`assembly_id`),
+  UNIQUE KEY `accession` (`accession`),
+  UNIQUE KEY `assembly_uuid` (`assembly_uuid`),
+  UNIQUE KEY `ensembl_name` (`ensembl_name`),
+  KEY `idx_assembly_name` (`name`)
+) ENGINE=InnoDB AUTO_INCREMENT=6404 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `assembly`
+--
+-- WHERE:  assembly_default = 'GRCh38';
+
+LOCK TABLES `assembly` WRITE;
+/*!40000 ALTER TABLE `assembly` DISABLE KEYS */;
+INSERT INTO `assembly` VALUES (92,'hg38','GCA_000001405.29','chromosome','GRCh38.p14',NULL,'GRCh38',NULL,'2023-09-22 15:04:45.000000','GRCh38.p14',NULL,'fd7fea38-981a-4d73-a879-6f9daef86f08',1,'grch38');
+/*!40000 ALTER TABLE `assembly` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `assembly_sequence`
+--
+
+DROP TABLE IF EXISTS `assembly_sequence`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `assembly_sequence` (
+  `assembly_sequence_id` int(11) NOT NULL AUTO_INCREMENT,
+  `name` varchar(128) DEFAULT NULL,
+  `accession` varchar(128) NOT NULL,
+  `chromosomal` tinyint(1) NOT NULL,
+  `length` int(11) NOT NULL,
+  `sequence_location` varchar(10) DEFAULT NULL,
+  `md5` varchar(32) DEFAULT NULL,
+  `assembly_id` int(11) NOT NULL,
+  `chromosome_rank` int(11) DEFAULT NULL,
+  `sha512t24u` varchar(128) DEFAULT NULL,
+  `is_circular` tinyint(1) DEFAULT '0',
+  `type` varchar(26) DEFAULT 'primary_assembly',
+  PRIMARY KEY (`assembly_sequence_id`),
+  UNIQUE KEY `assembly_sequence_assembly_id_accession_5f3e5119_uniq` (`assembly_id`,`accession`),
+  KEY `assembly_sequence_name_assembly_id_index` (`name`,`assembly_id`),
+  KEY `assembly_sequence_assembly_id_chromosomal_index` (`assembly_id`,`chromosomal`),
+  CONSTRAINT `assembly_sequence_assembly_id_2a84ddcb_fk_assembly_assembly_id` FOREIGN KEY (`assembly_id`) REFERENCES `assembly` (`assembly_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=59415596 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `assembly_sequence`
+--
+-- WHERE:  assembly_id = 92;
+
+LOCK TABLES `assembly_sequence` WRITE;
+/*!40000 ALTER TABLE `assembly_sequence` DISABLE KEYS */;
+INSERT INTO `assembly_sequence` VALUES 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+  `name` varchar(128) NOT NULL,
+  `label` varchar(128) NOT NULL,
+  `description` varchar(255) DEFAULT NULL,
+  `type` varchar(8) NOT NULL,
+  `required` tinyint(1) NOT NULL DEFAULT '0',
+  PRIMARY KEY (`attribute_id`),
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genome length','Total length of all genomic sequences','bp',0),(20,'assembly.ucsc_alias','assembly.ucsc_alias','assembly.ucsc_alias','string',0),(21,'genebuild.stats.average_cds_length','Average CDS length','Average length of coding sequences','float',0),(22,'genebuild.stats.average_coding_exons_per_coding_transcript','Average Coding Exons per coding transcript','Average Coding Exons per coding transcript','float',0),(23,'genebuild.stats.average_coding_exons_per_transcript','Average coding exons per transcript','Average coding exons per coding transcript','float',0),(24,'genebuild.stats.average_coding_exon_length','Average exon length per coding gene','Average length of coding exons','bp',0),(25,'genebuild.stats.average_exon_length','Average exon length','Average length of exons','bp',0),(26,'genebuild.stats.average_genomic_span','Average coding genomic span','Average length of all genomic regions','bp',0),(27,'genebuild.stats.average_intron_length','Average intron length','Average intron length per coding gene','bp',0),(28,'genebuild.average_sequence_legth','Average coding sequence length','Average length of sequences in genome','bp',0),(29,'genebuild.stats.coding_genes','Coding genes','Genes that code for proteins','integer',0),(30,'genebuild.stats.coding_transcripts','Coding transcripts','Transcripts that code for proteins','integer',0),(31,'genebuild.stats.coding_transcripts_per_gene','Average coding transcripts per gene','Average coding transcripts per gene','float',0),(32,'genebuild.hash','genebuild.hash','genebuild.hash','string',0),(33,'genebuild.initial_release_date','genebuild.initial_release_date','genebuild.initial_release_date','string',0),(34,'genebuild.last_geneset_update','genebuild.last_geneset_update','genebuild.last_geneset_update','string',1),(35,'genebuild.level','genebuild.level','genebuild.level','string',0),(36,'genebuild.stats.longest_gene_length','Longest coding gene','Length of longest 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body','Accessioning body if different from ena','string',0),(223,'faulty_reason','Faulty Reason','Reason why dataset is faulty','string',0),(224,'vep.ftp','VEP Files for FTP','Whether the data should be placed on the FTP','string',0);
+/*!40000 ALTER TABLE `attribute` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `dataset`
+--
+
+DROP TABLE IF EXISTS `dataset`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset` (
+  `dataset_id` int(11) NOT NULL AUTO_INCREMENT,
+  `dataset_uuid` varchar(40) NOT NULL,
+  `name` varchar(128) NOT NULL,
+  `version` varchar(128) DEFAULT NULL,
+  `created` datetime(6) NOT NULL,
+  `label` varchar(128) NOT NULL,
+  `dataset_source_id` int(11) NOT NULL,
+  `dataset_type_id` int(11) NOT NULL,
+  `status` varchar(12) NOT NULL,
+  `parent_id` int(11) DEFAULT NULL,
+  PRIMARY KEY (`dataset_id`),
+  UNIQUE KEY `dataset_dataset_uuid_b369a069_uniq` (`dataset_uuid`),
+  KEY `dataset_dataset_source_id_fd96f115_fk_dataset_s` (`dataset_source_id`),
+  KEY `dataset_dataset_type_id_47284562_fk_dataset_type_dataset_type_id` (`dataset_type_id`),
+  KEY `dataset_parent_id_fk` (`parent_id`),
+  CONSTRAINT `dataset_dataset_source_id_fd96f115_fk_dataset_s` FOREIGN KEY (`dataset_source_id`) REFERENCES `dataset_source` (`dataset_source_id`) ON DELETE CASCADE,
+  CONSTRAINT `dataset_dataset_type_id_47284562_fk_dataset_type_dataset_type_id` FOREIGN KEY (`dataset_type_id`) REFERENCES `dataset_type` (`dataset_type_id`),
+  CONSTRAINT `dataset_parent_id_fk` FOREIGN KEY (`parent_id`) REFERENCES `dataset` (`dataset_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=142152 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `dataset`
+--
+-- WHERE:  dataset_id in (select distinct(dataset_id) from genome_dataset where genome_id in (86, 5255))
+
+LOCK TABLES `dataset` WRITE;
+/*!40000 ALTER TABLE `dataset` DISABLE KEYS */;
+INSERT INTO `dataset` VALUES (171,'c813f7b7-645c-45ac-8536-08190fd7daa0','assembly',NULL,'2023-09-22 15:04:45.000000','GCA_000001405.29',92,1,'Released',NULL),(172,'949defef-c4d2-4ab1-8a73-f41d2b3c7719','genebuild','GENCODE44','2023-09-22 15:04:45.000000','GCA_000001405.29_GENCODE44',92,2,'Released',NULL),(2518,'679d6452-799c-4a2f-8906-0db6c639e498','regulatory_features','1.0','2023-11-15 15:07:12.410801','Regulatory Annotation',670,7,'Released',NULL),(61336,'c843b413-7943-4269-a661-6765335c75c8','compara_homologies','1.0','2024-03-26 15:12:42.825233','Compara homologies ',424,6,'Released',NULL),(63983,'b78f1a07-03e9-11ef-b152-005056b31e22','compara_homologies','2.0','2024-04-26 17:26:21.000000','Compara homologies ',424,6,'Released',NULL),(71789,'333d27f0-3ad4-434d-a7c7-02da49eabb0c','genebuild_compute','GENCODE44','2024-07-09 22:11:44.000000','From 949defef-c4d2-4ab1-8a73-f41d2b3c7719',92,8,'Released',172),(71790,'a92ac61c-4f04-4f80-a7da-e5269d0ad12c','xrefs','GENCODE44','2024-07-09 22:11:44.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,13,'Released',71789),(71791,'ea72608b-1242-49de-b85d-4d7e3f9f3d8f','protein_features','GENCODE44','2024-07-09 22:11:44.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,14,'Released',71789),(71792,'fcead08a-7c90-426a-9772-c3747dcf257e','alpha_fold','GENCODE44','2024-07-09 22:11:45.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,15,'Released',71789),(71793,'ac3d7922-39ec-43ec-a9ba-4ab28d5f1a8c','vep_cache','GENCODE44','2024-07-09 22:11:45.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,39,'Released',71789),(71794,'d4ac4bc8-2dd3-4c8b-8fe4-168eee59f45a','genebuild_files','GENCODE44','2024-07-09 22:11:45.000000','From 949defef-c4d2-4ab1-8a73-f41d2b3c7719',92,9,'Released',172),(71795,'6947d093-5d6c-4ee2-a58f-892647956fac','blast','GENCODE44','2024-07-09 22:11:46.000000','From 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14:19:25.000000','GRCh38',5796,3,'Released',NULL),(116190,'1126761b-14ef-4e3d-b453-778231513fba','track_handover',NULL,'2024-10-25 14:19:26.000000','From 317706bc-2a04-4ce5-aca5-f96d129a1b70',5796,31,'Released',116189),(127671,'46d6b8b7-aa08-4334-b00d-474fd49189b6','regulatory_features',NULL,'2025-04-16 14:12:19.000000','Regulatory Annotation',7282,7,'Released',NULL),(127672,'53cfea1a-9aca-4b7e-a5a7-2787805f005e','regulation_handover',NULL,'2025-04-16 14:12:19.000000','From 46d6b8b7-aa08-4334-b00d-474fd49189b6',7282,33,'Released',127671),(127673,'4e9b5e61-b0d9-4333-b83c-0ba0eb854f13','regulatory_features',NULL,'2025-04-16 14:13:38.000000','Regulatory Annotation',7282,7,'Released',NULL),(122649,'361aff67-f177-4bce-aaf4-be5ba3c0beef','genebuild','GENCODE48_subset','2025-02-24 11:21:59.000000','GCA_000001405.29_GENCODE48_subset',92,2,'Released',NULL),(122650,'bb5d83d0-c714-459d-bde6-479f38e69bee','compara_homologies','1.0','2025-02-24 11:21:59.000000','Compara homologies',424,6,'Released',NULL),(122651,'7f91437c-008e-4bf3-91ef-eb45c4e1c8f0','genebuild_compute','GENCODE48_subset','2025-02-24 11:21:59.000000','From 361aff67-f177-4bce-aaf4-be5ba3c0beef',92,8,'Released',122649),(122652,'eba5d7b6-9db0-41d0-a238-c0b8ee6ba25d','xrefs','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,13,'Released',122651),(122653,'a349b8ac-08e6-4337-bcfa-32d7bba0d5f9','protein_features','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,14,'Released',122651),(122654,'8a8b7b22-e3c1-4753-80d8-9d21511a586b','alpha_fold','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,15,'Released',122651),(122655,'28dadec5-679f-4547-9a29-aef2c8d1758a','vep_cache','GENCODE48_subset','2025-02-24 11:21:59.000000','From 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+/*!40000 ALTER TABLE `dataset` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `dataset_attribute`
+--
+
+DROP TABLE IF EXISTS `dataset_attribute`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset_attribute` (
+  `dataset_attribute_id` int(11) NOT NULL AUTO_INCREMENT,
+  `value` varchar(255) DEFAULT NULL,
+  `attribute_id` int(11) NOT NULL,
+  `dataset_id` int(11) NOT NULL,
+  PRIMARY KEY (`dataset_attribute_id`),
+  UNIQUE KEY `dataset_attribute_dataset_id_attribute_id_value_4d1ddfaf_uniq` (`dataset_id`,`attribute_id`,`value`),
+  KEY `dataset_attribute_attribute_id_55c51407_fk_attribute` (`attribute_id`),
+  KEY `dataset_attribute_dataset_id_2e2afe19` (`dataset_id`),
+  CONSTRAINT `dataset_attribute_attribute_id_55c51407_fk_attribute` FOREIGN KEY (`attribute_id`) REFERENCES `attribute` (`attribute_id`) ON DELETE CASCADE,
+  CONSTRAINT `dataset_attribute_dataset_id_2e2afe19_fk_dataset_dataset_id` FOREIGN KEY (`dataset_id`) REFERENCES `dataset` (`dataset_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=677594 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `dataset_attribute`
+--
+-- WHERE:  dataset_id in (select distinct(dataset_id) from genome_dataset where genome_id in (86, 5255))
+
+LOCK TABLES `dataset_attribute` WRITE;
+/*!40000 ALTER TABLE `dataset_attribute` DISABLE KEYS */;
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+DROP TABLE IF EXISTS `dataset_source`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset_source` (
+  `dataset_source_id` int(11) NOT NULL AUTO_INCREMENT,
+  `type` varchar(32) NOT NULL,
+  `name` varchar(255) NOT NULL,
+  PRIMARY KEY (`dataset_source_id`),
+  UNIQUE KEY `name` (`name`)
+) ENGINE=InnoDB AUTO_INCREMENT=9131 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
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+LOCK TABLES `dataset_source` WRITE;
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diff --git a/nextflow/vcf_prepper/tests/testdata/homo_sapiens_GRCh38.chrom.sizes b/nextflow/vcf_prepper/tests/testdata/homo_sapiens_GRCh38.chrom.sizes
new file mode 100755
index 00000000..16332dfd
--- /dev/null
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+HSCHR19KIR_GRC212_AB_HAP_CTG3_1	209513
+HSCHR19KIR_GRC212_BA1_HAP_CTG3_1	155533
+HSCHR19KIR_LUCE_A_HAP_CTG3_1	170699
+HSCHR19KIR_LUCE_BDEL_HAP_CTG3_1	184500
+HSCHR19KIR_RSH_A_HAP_CTG3_1	170681
+HSCHR19KIR_RSH_BA2_HAP_CTG3_1	205195
+HSCHR19KIR_T7526_A_HAP_CTG3_1	170666
+HSCHR19KIR_T7526_BDEL_HAP_CTG3_1	184517
+HSCHR19KIR_ABC08_A1_HAP_CTG3_1	190933
+HSCHR19KIR_ABC08_AB_HAP_C_P_CTG3_1	123112
+HSCHR19KIR_ABC08_AB_HAP_T_P_CTG3_1	170702
+HSCHR19KIR_FH05_A_HAP_CTG3_1	198006
+HSCHR19KIR_FH05_B_HAP_CTG3_1	282225
+HSCHR19KIR_FH06_A_HAP_CTG3_1	187936
+HSCHR19KIR_FH06_BA1_HAP_CTG3_1	189353
+HSCHR19KIR_FH08_A_HAP_CTG3_1	186204
+HSCHR19KIR_FH08_BAX_HAP_CTG3_1	200774
+HSCHR19KIR_FH13_A_HAP_CTG3_1	170149
+HSCHR19KIR_FH13_BA2_HAP_CTG3_1	215733
+HSCHR19KIR_FH15_A_HAP_CTG3_1	170538
+HSCHR19KIR_RP5_B_HAP_CTG3_1	177382
+NC_012920	16570
+HG2095_PATCH	305543
+HG2058_PATCH	166201
+HG986_PATCH	186495
+HG2104_PATCH	122023
+HG1832_PATCH	460101
+HG2232_PATCH	365500
+HG2233_PATCH	208150
+HG2066_PATCH	451169
+HG126_PATCH	415309
+HG2022_PATCH	305980
+HSCHR5_7_CTG1	139088
+HG2128_PATCH	268331
+HG2030_PATCH	330165
+HG2244_HG2245_PATCH	420165
+HG2191_PATCH	277798
+HG2242_HG2243_PATCH	85285
+HG2241_PATCH	14348
+HSCHR11_1_CTG1_2	203553
+HG2217_PATCH	108876
+HG1362_PATCH	541039
+HG23_PATCH	211378
+HG2247_PATCH	86534
+HG2291_PATCH	356767
+HG2216_PATCH	35456
+HG2249_PATCH	148763
+HG2288_HG2289_PATCH	206321
+HG2021_PATCH	370918
+HSCHR22_4_CTG1	156563
+HSCHR22_5_CTG1	153028
+HG2062_PATCH	101151
+HG1342_HG2282_PATCH	467144
+HG2290_PATCH	481246
+HG2235_PATCH	373700
+HG2237_PATCH	165719
+HG1651_PATCH	320751
+HG2239_PATCH	179933
+HSCHR15_6_CTG8	2365365
+HSCHR16_3_CTG3_1	169137
+HSCHR1_4_CTG3	349939
+HSCHR1_3_CTG3	141020
+HSCHR1_5_CTG32_1	212206
+HSCHR4_2_CTG4	90923
+HSCHR4_8_CTG12	163750
+HSCHR4_9_CTG12	236513
+HSCHR6_1_CTG10	82316
+HG2072_PATCH	245717
+HSCHR9_1_CTG6	163883
+HSCHR9_1_CTG7	134100
+HSCHR10_1_CTG6	185508
+HG2334_PATCH	264546
+HG2116_PATCH	181959
+HSCHR12_2_CTG1	109324
+HSCHR13_1_CTG7	168147
+HSCHR13_1_CTG8	123481
+HSCHR16_5_CTG1	59017
+HSCHR16_4_CTG3_1	267464
+HSCHR18_5_CTG1_1	205102
+HG2213_PATCH	407388
+HG26_PATCH	405390
+HSCHR22_6_CTG1	155931
+HSCHR22_7_CTG1	174750
+HSCHR1_5_CTG3	278660
+HSCHR2_6_CTG7_2	535089
+HG2023_PATCH	230435
+HSCHR4_11_CTG12	205408
+HG2063_PATCH	315611
+HSCHR22_8_CTG1	145163
+HG1343_HG173_HG459_PATCH	1572687
+HSCHR1_12_CTG3	516765
+HSCHR1_6_CTG3	551021
+HG2236_PATCH	411655
+HSCHR4_12_CTG12	420676
+HSCHR5_8_CTG1	362222
+HG30_PATCH	673060
+HG2088_PATCH	142130
+HG2266_PATCH	468268
+HG2068_PATCH	265877
+HG2067_PATCH	156999
+HG1708_PATCH	140878
+HG926_PATCH	1927116
+HG2285_HG106_HG2252_PATCH	281920
+HG2046_PATCH	154724
+HSCHR17_3_CTG1	276293
+HSCHR17_11_CTG4	246896
+HSCHR19KIR_0019-4656-A_CTG3_1	163927
+HSCHR19KIR_CA01-TA01_1_CTG3_1	170207
+HSCHR19KIR_CA01-TA01_2_CTG3_1	168132
+HSCHR19KIR_CA01-TB04_CTG3_1	293523
+HSCHR19KIR_CA01-TB01_CTG3_1	241059
+HSCHR19KIR_HG2394_CTG3_1	159286
+HSCHR19KIR_502960008-2_CTG3_1	178198
+HSCHR19KIR_502960008-1_CTG3_1	166714
+HSCHR19KIR_0010-5217-AB_CTG3_1	99846
+HSCHR19KIR_7191059-1_CTG3_1	161096
+HSCHR19KIR_0019-4656-B_CTG3_1	223119
+HSCHR19KIR_CA04_CTG3_1	100554
+HSCHR19KIR_7191059-2_CTG3_1	171264
+HSCHR19KIR_HG2396_CTG3_1	145692
+HSCHR19KIR_HG2393_CTG3_1	156966
+HSCHRX_3_CTG7	188005
+HSCHR1_8_CTG3	166137
+HSCHR1_9_CTG3	140356
+HG2002_PATCH	330032
+HSCHR2_7_CTG7_2	181659
+HSCHR2_8_CTG7_2	140362
+HSCHR3_4_CTG1	175850
+HSCHR5_9_CTG1	135988
+HG2057_PATCH	242797
+HG708_PATCH	589657
+HSCHR7_3_CTG4_4	680663
+HG76_PATCH	6367529
+HG2419_PATCH	165121
+HG1815_PATCH	1046839
+HSCHR12_8_CTG2_1	174809
+HG2047_PATCH	64690
+HG1_PATCH	690933
+HSCHR14_8_CTG1	171799
+HSCHR16_5_CTG3_1	78610
+HG2442_PATCH	93071
+HG1531_PATCH	48371
+HG1535_PATCH	209723
+HG460_PATCH	44956
+HG2133_PATCH	105528
+HSCHR3_6_CTG2_1	195064
+HSCHR3_9_CTG2_1	302886
+HSCHR3_8_CTG2_1	197753
+HSCHR3_7_CTG2_1	164042
+HSCHR7_3_CTG1	172556
+HSCHR8_7_CTG7	103073
+HG2114_PATCH	279645
+HG2060_PATCH	305245
+HSCHR11_1_CTG3_1	181168
+HSCHR11_2_CTG8	301638
+HSCHR12_9_CTG2_1	154140
+HG2263_PATCH	480416
+HSCHR17_12_CTG4	116754
+HSCHR18_1_CTG1	163187
+HG2412_PATCH	230844
+HG1384_PATCH	84044
+HG721_PATCH	145976
+HSCHR3_5_CTG1	215444
+HG699_PATCH	235735
+HG1298_PATCH	176675
+HG1299_PATCH	53477
+HG1296_PATCH	125550
+HG2525_PATCH	341067
+HG705_PATCH	276110
+HG1395_PATCH	89957
+HG2121_PATCH	139428
+HG563_PATCH	73266
+HG1309_PATCH	254760
+HG613_PATCH	25409
+HG545_PATCH	454964
+HG1277_PATCH	292945
+HG28_PATCH	270123
+HG2111_PATCH	170929
+HG2115_PATCH	217076
+HG1445_PATCH	165420
+HG1521_PATCH	45258
+HG1398_PATCH	192532
+HG2246_HG2248_HG2276_PATCH	297569
+HG2509_PATCH	409913
+HG1817_1_PATCH	7310
+HG1523_PATCH	158945
+HG1524_PATCH	65395
+HG2510_PATCH	399184
+HSCHR14_9_CTG1	264229
+HG2511_PATCH	396516
+HG2365_PATCH	5500450
+HG2198_PATCH	369265
+HG2499_PATCH	97764
+HG2471_PATCH	270968
+HG2087_PATCH	137909
+HG1320_PATCH	56696
+HG109_PATCH	493166
+HG2513_PATCH	519486
+HG2512_PATCH	412369
+HG1485_PATCH	461304
+HG494_PATCH	12296
+HG1466_PATCH	17436
+HG1506_PATCH	28825
+HG1507_PATCH	68193
+HG439_PATCH	403129
+HG1509_PATCH	14679
+HG2515_PATCH	211935
+HG2577_PATCH	250448
+HSCHR1_5_CTG31	847442
+HG2571_PATCH	210427
+HSCHR1_6_CTG31	335160
+HG2231_HG2496_PATCH	244726
+HG2140_PATCH	174386
+HG2052_PATCH	489405
+HSCHR2_6_CTG1	284972
+HSCHR2_10_CTG7_2	431783
+HG2275_PATCH	955088
+HSCHR2_12_CTG7_2	500582
+HSCHR2_11_CTG7_2	535252
+HG2494_PATCH	120382
+HG2077_PATCH	301311
+HG2069_PATCH	475877
+HG2264_PATCH	469343
+HG287_PATCH	205692
+HSCHR4_2_CTG8_1	308683
+HG2155_PATCH	113365
+HG2476_PATCH	208406
+HSCHR5_10_CTG1	302486
+HG2308_PATCH	508333
+HG1046_PATCH	34401
+HSCHR6_1_CTG1	383129
+HSCHR7_4_CTG1	464418
+HG2267_PATCH	429745
+HG2176_PATCH	150303
+HG2408_PATCH	106906
+HG2031_PATCH	207372
+HG1047_PATCH	39291
+HG1206_PATCH	569669
+HG2158_PATCH	340718
+HG1012_PATCH	482251
+HG2576_PATCH	196263
+HG107_HG2565_PATCH	205000
+HG152_PATCH	434832
+HG2578_PATCH	122723
+HG2568_PATCH	344607
+HSCHR11_2_CTG3_1	261195
+HG2554_PATCH	104538
+HG2526_HG2573_PATCH	722646
+HSCHR15_9_CTG8	204008
+HG2280_PATCH	1154575
+HG401_PATCH	87716
+HG405_PATCH	334998
+HG2407_PATCH	538542
+HSCHR17_13_CTG4	372840
+HG2580_PATCH	172610
+HG2118_PATCH	234879
+HG1369_PATCH	187627
+HG2251_PATCH	144690
+HSCHR19_6_CTG2	89212
+HG2461_PATCH	333755
+HG2569_PATCH	137819
+HG2225_PATCH	273726
+HG410_PATCH	355732
+HG2219_PATCH	336753
+HG2265_PATCH	1020779
+HG2521_PATCH	189708
+HG1311_HG2539_PATCH	101041
+HSCHRX_3_CTG3	330494
+HG2527_PATCH	68811
+HG2541_PATCH	140568
+HSCHRX_2_CTG14	294120
+HSCHRX_1_CTG14	619717
+HG1532_PATCH	865744
+19	58617617
+20	64444168
+X	156040896
+9	138394718
+13	114364329
+5	181538260
+21	46709984
+10	133797423
+2	242193530
+12	133275310
+14	107043719
+18	80373286
+16	90338346
+1	248956423
+3	198295560
+4	190214556
+Y	57227416
+17	83257442
+6	170805980
+11	135086623
+22	50818469
+15	101991190
+7	159345974
+8	145138637
+MT	16570
+chr1	248956423
+chr10	133797423
+chr10_GL383545v1_alt	179255
+chr10_GL383546v1_alt	309803
+chr10_KI270824v1_alt	181497
+chr10_KI270825v1_alt	188316
+chr10_KN196480v1_fix	277798
+chr10_KN538365v1_fix	14348
+chr10_KN538366v1_fix	85285
+chr10_KN538367v1_fix	420165
+chr10_KQ090020v1_alt	185508
+chr10_KQ090021v1_fix	264546
+chr10_ML143354v1_fix	454964
+chr10_ML143355v1_fix	292945
+chr10_MU273367v1_fix	196263
+chr11	135086623
+chr11_GL383547v1_alt	154408
+chr11_JH159136v1_alt	200999
+chr11_JH159137v1_alt	191410
+chr11_KI270721v1_random	100317
+chr11_KI270826v1_alt	186170
+chr11_KI270827v1_alt	67708
+chr11_KI270829v1_alt	204060
+chr11_KI270830v1_alt	177093
+chr11_KI270831v1_alt	296896
+chr11_KI270832v1_alt	210134
+chr11_KI270902v1_alt	106712
+chr11_KI270903v1_alt	214626
+chr11_KI270927v1_alt	218613
+chr11_KN196481v1_fix	108876
+chr11_KN538368v1_alt	203553
+chr11_KQ090022v1_fix	181959
+chr11_KQ759759v2_fix	205000
+chr11_KV766195v1_fix	140878
+chr11_KZ559108v1_fix	305245
+chr11_KZ559109v1_fix	279645
+chr11_KZ559110v1_alt	301638
+chr11_KZ559111v1_alt	181168
+chr11_ML143356v1_fix	45258
+chr11_ML143357v1_fix	165420
+chr11_ML143358v1_fix	270123
+chr11_ML143359v1_fix	217076
+chr11_ML143360v1_fix	170929
+chr11_MU273368v1_alt	261195
+chr11_MU273369v1_fix	434832
+chr11_MU273370v1_fix	344607
+chr11_MU273371v1_fix	122723
+chr12	133275310
+chr12_GL383549v1_alt	120805
+chr12_GL383550v2_alt	169179
+chr12_GL383551v1_alt	184320
+chr12_GL383552v1_alt	138656
+chr12_GL383553v2_alt	152875
+chr12_GL877875v1_alt	167314
+chr12_GL877876v1_alt	408272
+chr12_KI270833v1_alt	76062
+chr12_KI270834v1_alt	119499
+chr12_KI270835v1_alt	238140
+chr12_KI270836v1_alt	56135
+chr12_KI270837v1_alt	40091
+chr12_KI270904v1_alt	572350
+chr12_KN196482v1_fix	211378
+chr12_KN538369v1_fix	541039
+chr12_KN538370v1_fix	86534
+chr12_KQ090023v1_alt	109324
+chr12_KQ759760v1_fix	315611
+chr12_KZ208916v1_fix	1046839
+chr12_KZ208917v1_fix	64690
+chr12_KZ208918v1_alt	174809
+chr12_KZ559112v1_alt	154140
+chr12_ML143361v1_fix	297569
+chr12_ML143362v1_fix	192532
+chr12_MU273372v1_fix	104538
+chr13	114364329
+chr13_KI270838v1_alt	306914
+chr13_KI270839v1_alt	180307
+chr13_KI270840v1_alt	191685
+chr13_KI270841v1_alt	169135
+chr13_KI270842v1_alt	37288
+chr13_KI270843v1_alt	103833
+chr13_KN196483v1_fix	35456
+chr13_KN538371v1_fix	206321
+chr13_KN538372v1_fix	356767
+chr13_KN538373v1_fix	148763
+chr13_KQ090024v1_alt	168147
+chr13_KQ090025v1_alt	123481
+chr13_ML143363v1_fix	7310
+chr13_ML143364v1_fix	158945
+chr13_ML143365v1_fix	65395
+chr13_ML143366v1_fix	409913
+chr14	107043719
+chr14_GL000009v2_random	201710
+chr14_GL000194v1_random	191470
+chr14_GL000225v1_random	211174
+chr14_KI270722v1_random	194051
+chr14_KI270723v1_random	38116
+chr14_KI270724v1_random	39556
+chr14_KI270725v1_random	172811
+chr14_KI270726v1_random	43740
+chr14_KI270844v1_alt	322167
+chr14_KI270845v1_alt	180704
+chr14_KI270846v1_alt	1351394
+chr14_KI270847v1_alt	1511112
+chr14_KZ208919v1_alt	171799
+chr14_KZ208920v1_fix	690933
+chr14_ML143367v1_fix	399184
+chr14_ML143368v1_alt	264229
+chr14_MU273373v1_fix	722646
+chr15	101991190
+chr15_GL383554v1_alt	296528
+chr15_GL383555v2_alt	388774
+chr15_KI270727v1_random	448249
+chr15_KI270848v1_alt	327383
+chr15_KI270849v1_alt	244918
+chr15_KI270850v1_alt	430881
+chr15_KI270851v1_alt	263055
+chr15_KI270852v1_alt	479000
+chr15_KI270905v1_alt	5161415
+chr15_KI270906v1_alt	196385
+chr15_KQ031389v1_alt	2365365
+chr15_ML143369v1_fix	97764
+chr15_ML143370v1_fix	369265
+chr15_ML143371v1_fix	5500450
+chr15_ML143372v1_fix	396516
+chr15_MU273374v1_fix	1154575
+chr15_MU273375v1_alt	204008
+chr16	90338346
+chr16_GL383556v1_alt	192463
+chr16_GL383557v1_alt	89673
+chr16_KI270728v1_random	1872760
+chr16_KI270853v1_alt	2659701
+chr16_KI270854v1_alt	134194
+chr16_KI270855v1_alt	232858
+chr16_KI270856v1_alt	63983
+chr16_KQ031390v1_alt	169137
+chr16_KQ090026v1_alt	59017
+chr16_KQ090027v1_alt	267464
+chr16_KV880768v1_fix	1927116
+chr16_KZ208921v1_alt	78610
+chr16_KZ559113v1_fix	480416
+chr16_ML143373v1_fix	270968
+chr16_MU273376v1_fix	87716
+chr16_MU273377v1_fix	334998
+chr17	83257442
+chr17_GL000205v2_random	185592
+chr17_GL000258v2_alt	1821993
+chr17_GL383563v3_alt	375692
+chr17_GL383564v2_alt	133152
+chr17_GL383565v1_alt	223996
+chr17_GL383566v1_alt	90220
+chr17_JH159146v1_alt	278132
+chr17_JH159147v1_alt	70346
+chr17_JH159148v1_alt	88071
+chr17_KI270729v1_random	280840
+chr17_KI270730v1_random	112552
+chr17_KI270857v1_alt	2877075
+chr17_KI270858v1_alt	235828
+chr17_KI270859v1_alt	108764
+chr17_KI270860v1_alt	178922
+chr17_KI270861v1_alt	196689
+chr17_KI270862v1_alt	391358
+chr17_KI270907v1_alt	137722
+chr17_KI270908v1_alt	1423191
+chr17_KI270909v1_alt	325801
+chr17_KI270910v1_alt	157100
+chr17_KV575245v1_fix	154724
+chr17_KV766196v1_fix	281920
+chr17_KV766197v1_alt	246896
+chr17_KV766198v1_alt	276293
+chr17_KZ559114v1_alt	116754
+chr17_ML143374v1_fix	137909
+chr17_ML143375v1_fix	56696
+chr17_MU273378v1_alt	372840
+chr17_MU273379v1_fix	234879
+chr17_MU273380v1_fix	538542
+chr17_MU273381v1_fix	144690
+chr17_MU273382v1_fix	187627
+chr17_MU273383v1_fix	172610
+chr18	80373286
+chr18_GL383567v1_alt	289832
+chr18_GL383568v1_alt	104553
+chr18_GL383569v1_alt	167951
+chr18_GL383570v1_alt	164790
+chr18_GL383571v1_alt	198279
+chr18_GL383572v1_alt	159548
+chr18_KI270863v1_alt	168000
+chr18_KI270864v1_alt	111738
+chr18_KI270911v1_alt	157711
+chr18_KI270912v1_alt	174062
+chr18_KQ090028v1_fix	407388
+chr18_KQ458385v1_alt	205102
+chr18_KZ208922v1_fix	93071
+chr18_KZ559115v1_fix	230844
+chr18_KZ559116v1_alt	163187
+chr19	58617617
+chr19_GL000209v2_alt	177382
+chr19_GL383573v1_alt	385658
+chr19_GL383574v1_alt	155865
+chr19_GL383575v2_alt	170223
+chr19_GL383576v1_alt	188025
+chr19_GL949746v1_alt	987717
+chr19_GL949747v2_alt	729521
+chr19_GL949748v2_alt	1064305
+chr19_GL949749v2_alt	1091842
+chr19_GL949750v2_alt	1066391
+chr19_GL949751v2_alt	1002684
+chr19_GL949752v1_alt	987101
+chr19_GL949753v2_alt	796480
+chr19_KI270865v1_alt	52970
+chr19_KI270866v1_alt	43157
+chr19_KI270867v1_alt	233763
+chr19_KI270868v1_alt	61735
+chr19_KI270882v1_alt	248808
+chr19_KI270883v1_alt	170400
+chr19_KI270884v1_alt	157054
+chr19_KI270885v1_alt	171028
+chr19_KI270886v1_alt	204240
+chr19_KI270887v1_alt	209513
+chr19_KI270888v1_alt	155533
+chr19_KI270889v1_alt	170699
+chr19_KI270890v1_alt	184500
+chr19_KI270891v1_alt	170681
+chr19_KI270914v1_alt	205195
+chr19_KI270915v1_alt	170666
+chr19_KI270916v1_alt	184517
+chr19_KI270917v1_alt	190933
+chr19_KI270918v1_alt	123112
+chr19_KI270919v1_alt	170702
+chr19_KI270920v1_alt	198006
+chr19_KI270921v1_alt	282225
+chr19_KI270922v1_alt	187936
+chr19_KI270923v1_alt	189353
+chr19_KI270929v1_alt	186204
+chr19_KI270930v1_alt	200774
+chr19_KI270931v1_alt	170149
+chr19_KI270932v1_alt	215733
+chr19_KI270933v1_alt	170538
+chr19_KI270938v1_alt	1066801
+chr19_KN196484v1_fix	370918
+chr19_KQ458386v1_fix	405390
+chr19_KV575246v1_alt	163927
+chr19_KV575247v1_alt	170207
+chr19_KV575248v1_alt	168132
+chr19_KV575249v1_alt	293523
+chr19_KV575250v1_alt	241059
+chr19_KV575251v1_alt	159286
+chr19_KV575252v1_alt	178198
+chr19_KV575253v1_alt	166714
+chr19_KV575254v1_alt	99846
+chr19_KV575255v1_alt	161096
+chr19_KV575256v1_alt	223119
+chr19_KV575257v1_alt	100554
+chr19_KV575258v1_alt	156966
+chr19_KV575259v1_alt	171264
+chr19_KV575260v1_alt	145692
+chr19_ML143376v1_fix	493166
+chr19_MU273384v1_fix	333755
+chr19_MU273385v1_fix	137819
+chr19_MU273387v1_alt	89212
+chr1_GL383518v1_alt	182440
+chr1_GL383519v1_alt	110269
+chr1_GL383520v2_alt	366581
+chr1_KI270706v1_random	175056
+chr1_KI270707v1_random	32033
+chr1_KI270708v1_random	127683
+chr1_KI270709v1_random	66861
+chr1_KI270710v1_random	40177
+chr1_KI270711v1_random	42211
+chr1_KI270712v1_random	176044
+chr1_KI270713v1_random	40746
+chr1_KI270714v1_random	41718
+chr1_KI270759v1_alt	425602
+chr1_KI270760v1_alt	109529
+chr1_KI270761v1_alt	165835
+chr1_KI270762v1_alt	354445
+chr1_KI270763v1_alt	911659
+chr1_KI270764v1_alt	50259
+chr1_KI270765v1_alt	185286
+chr1_KI270766v1_alt	256272
+chr1_KI270892v1_alt	162213
+chr1_KN196472v1_fix	186495
+chr1_KN196473v1_fix	166201
+chr1_KN196474v1_fix	122023
+chr1_KN538360v1_fix	460101
+chr1_KN538361v1_fix	305543
+chr1_KQ031383v1_fix	467144
+chr1_KQ458382v1_alt	141020
+chr1_KQ458383v1_alt	349939
+chr1_KQ458384v1_alt	212206
+chr1_KQ983255v1_alt	278660
+chr1_KV880763v1_alt	551021
+chr1_KZ208904v1_alt	166137
+chr1_KZ208905v1_alt	140356
+chr1_KZ208906v1_fix	330032
+chr1_KZ559100v1_fix	44956
+chr1_MU273330v1_alt	516765
+chr1_MU273331v1_alt	847442
+chr1_MU273332v1_alt	335160
+chr1_MU273333v1_fix	1572687
+chr1_MU273334v1_fix	210427
+chr1_MU273335v1_fix	211935
+chr1_MU273336v1_fix	250448
+chr2	242193530
+chr20	64444168
+chr20_GL383577v2_alt	128387
+chr20_KI270869v1_alt	118775
+chr20_KI270870v1_alt	183434
+chr20_KI270871v1_alt	58662
+chr20_MU273388v1_fix	273726
+chr20_MU273389v1_fix	355732
+chr21	46709984
+chr21_GL383578v2_alt	63918
+chr21_GL383579v2_alt	201198
+chr21_GL383580v2_alt	74654
+chr21_GL383581v2_alt	116690
+chr21_KI270872v1_alt	82693
+chr21_KI270873v1_alt	143901
+chr21_KI270874v1_alt	166744
+chr21_ML143377v1_fix	519486
+chr21_MU273390v1_fix	336753
+chr21_MU273391v1_fix	1020779
+chr21_MU273392v1_fix	189708
+chr22	50818469
+chr22_GL383582v2_alt	162812
+chr22_GL383583v2_alt	96925
+chr22_KB663609v1_alt	74014
+chr22_KI270731v1_random	150755
+chr22_KI270732v1_random	41544
+chr22_KI270733v1_random	179773
+chr22_KI270734v1_random	165051
+chr22_KI270735v1_random	42812
+chr22_KI270736v1_random	181921
+chr22_KI270737v1_random	103839
+chr22_KI270738v1_random	99376
+chr22_KI270739v1_random	73986
+chr22_KI270875v1_alt	259915
+chr22_KI270876v1_alt	263667
+chr22_KI270877v1_alt	101332
+chr22_KI270878v1_alt	186263
+chr22_KI270879v1_alt	304136
+chr22_KI270928v1_alt	176104
+chr22_KN196485v1_alt	156563
+chr22_KN196486v1_alt	153028
+chr22_KQ458387v1_alt	155931
+chr22_KQ458388v1_alt	174750
+chr22_KQ759761v1_alt	145163
+chr22_KQ759762v2_fix	101041
+chr22_ML143378v1_fix	461304
+chr22_ML143379v1_fix	12296
+chr22_ML143380v1_fix	412369
+chr2_GL383521v1_alt	143391
+chr2_GL383522v1_alt	123822
+chr2_GL582966v2_alt	96132
+chr2_KI270715v1_random	161472
+chr2_KI270716v1_random	153800
+chr2_KI270767v1_alt	161579
+chr2_KI270768v1_alt	110100
+chr2_KI270769v1_alt	120617
+chr2_KI270770v1_alt	136241
+chr2_KI270771v1_alt	110396
+chr2_KI270772v1_alt	133042
+chr2_KI270773v1_alt	70888
+chr2_KI270774v1_alt	223626
+chr2_KI270775v1_alt	138020
+chr2_KI270776v1_alt	174167
+chr2_KI270893v1_alt	161219
+chr2_KI270894v1_alt	214159
+chr2_KN538362v1_fix	208150
+chr2_KN538363v1_fix	365500
+chr2_KQ031384v1_fix	481246
+chr2_KQ983256v1_alt	535089
+chr2_KZ208907v1_alt	181659
+chr2_KZ208908v1_alt	140362
+chr2_ML143341v1_fix	145976
+chr2_ML143342v1_fix	84044
+chr2_MU273337v1_alt	431783
+chr2_MU273338v1_alt	535252
+chr2_MU273339v1_alt	500582
+chr2_MU273340v1_alt	284972
+chr2_MU273341v1_fix	120382
+chr2_MU273342v1_fix	955088
+chr2_MU273343v1_fix	489405
+chr2_MU273344v1_fix	244726
+chr2_MU273345v1_fix	174386
+chr3	198295560
+chr3_GL000221v1_random	155398
+chr3_GL383526v1_alt	180672
+chr3_JH636055v2_alt	173152
+chr3_KI270777v1_alt	173650
+chr3_KI270778v1_alt	248253
+chr3_KI270779v1_alt	205313
+chr3_KI270780v1_alt	224109
+chr3_KI270781v1_alt	113035
+chr3_KI270782v1_alt	162430
+chr3_KI270783v1_alt	109188
+chr3_KI270784v1_alt	184405
+chr3_KI270895v1_alt	162897
+chr3_KI270924v1_alt	166541
+chr3_KI270934v1_alt	163459
+chr3_KI270935v1_alt	197352
+chr3_KI270936v1_alt	164171
+chr3_KI270937v1_alt	165608
+chr3_KN196475v1_fix	451169
+chr3_KN196476v1_fix	305980
+chr3_KN538364v1_fix	415309
+chr3_KQ031385v1_fix	373700
+chr3_KQ031386v1_fix	165719
+chr3_KV766192v1_fix	411655
+chr3_KZ208909v1_alt	175850
+chr3_KZ559101v1_alt	164042
+chr3_KZ559102v1_alt	197753
+chr3_KZ559103v1_alt	302886
+chr3_KZ559104v1_fix	105528
+chr3_KZ559105v1_alt	195064
+chr3_ML143343v1_alt	215444
+chr3_MU273346v1_fix	469343
+chr3_MU273347v1_fix	301311
+chr3_MU273348v1_fix	475877
+chr4	190214556
+chr4_GL000008v2_random	209710
+chr4_GL000257v2_alt	586477
+chr4_GL383527v1_alt	164537
+chr4_GL383528v1_alt	376188
+chr4_KI270785v1_alt	119913
+chr4_KI270786v1_alt	244097
+chr4_KI270787v1_alt	111944
+chr4_KI270788v1_alt	158966
+chr4_KI270789v1_alt	205945
+chr4_KI270790v1_alt	220247
+chr4_KI270896v1_alt	378548
+chr4_KI270925v1_alt	555800
+chr4_KQ090013v1_alt	90923
+chr4_KQ090014v1_alt	163750
+chr4_KQ090015v1_alt	236513
+chr4_KQ983257v1_fix	230435
+chr4_KQ983258v1_alt	205408
+chr4_KV766193v1_alt	420676
+chr4_ML143344v1_fix	235735
+chr4_ML143345v1_fix	341067
+chr4_ML143346v1_fix	53477
+chr4_ML143347v1_fix	176675
+chr4_ML143348v1_fix	125550
+chr4_ML143349v1_fix	276110
+chr4_MU273349v1_alt	308683
+chr4_MU273350v1_fix	113365
+chr4_MU273351v1_fix	205692
+chr5	181538260
+chr5_GL000208v1_random	92690
+chr5_GL339449v2_alt	1612929
+chr5_GL383530v1_alt	101242
+chr5_GL383531v1_alt	173460
+chr5_GL383532v1_alt	82729
+chr5_GL949742v1_alt	226853
+chr5_KI270791v1_alt	195711
+chr5_KI270792v1_alt	179044
+chr5_KI270793v1_alt	126137
+chr5_KI270794v1_alt	164559
+chr5_KI270795v1_alt	131893
+chr5_KI270796v1_alt	172709
+chr5_KI270897v1_alt	1144419
+chr5_KI270898v1_alt	130958
+chr5_KN196477v1_alt	139088
+chr5_KV575243v1_alt	362222
+chr5_KV575244v1_fix	673060
+chr5_KZ208910v1_alt	135988
+chr5_ML143350v1_fix	89957
+chr5_MU273352v1_fix	34401
+chr5_MU273353v1_fix	208406
+chr5_MU273355v1_fix	508333
+chr5_MU273356v1_alt	302486
+chr6	170805980
+chr6_GL000250v2_alt	4672375
+chr6_GL000251v2_alt	4795266
+chr6_GL000252v2_alt	4604812
+chr6_GL000253v2_alt	4677644
+chr6_GL000254v2_alt	4827814
+chr6_GL000255v2_alt	4606389
+chr6_GL000256v2_alt	4929270
+chr6_GL383533v1_alt	124737
+chr6_KB021644v2_alt	185824
+chr6_KI270758v1_alt	76753
+chr6_KI270797v1_alt	197537
+chr6_KI270798v1_alt	271783
+chr6_KI270799v1_alt	152149
+chr6_KI270800v1_alt	175809
+chr6_KI270801v1_alt	870481
+chr6_KI270802v1_alt	75006
+chr6_KN196478v1_fix	268331
+chr6_KQ031387v1_fix	320751
+chr6_KQ090016v1_fix	245717
+chr6_KQ090017v1_alt	82316
+chr6_KV766194v1_fix	139428
+chr6_KZ208911v1_fix	242797
+chr6_ML143351v1_fix	73266
+chr6_MU273357v1_alt	383129
+chr7	159345974
+chr7_GL383534v2_alt	119184
+chr7_KI270803v1_alt	1111571
+chr7_KI270804v1_alt	157953
+chr7_KI270805v1_alt	209989
+chr7_KI270806v1_alt	158167
+chr7_KI270807v1_alt	126435
+chr7_KI270808v1_alt	271456
+chr7_KI270809v1_alt	209587
+chr7_KI270899v1_alt	190870
+chr7_KQ031388v1_fix	179933
+chr7_KV880764v1_fix	142130
+chr7_KV880765v1_fix	468268
+chr7_KZ208912v1_fix	589657
+chr7_KZ208913v1_alt	680663
+chr7_KZ559106v1_alt	172556
+chr7_ML143352v1_fix	254760
+chr7_MU273358v1_alt	464418
+chr8	145138637
+chr8_KI270810v1_alt	374416
+chr8_KI270811v1_alt	292437
+chr8_KI270812v1_alt	282737
+chr8_KI270813v1_alt	300231
+chr8_KI270814v1_alt	141813
+chr8_KI270815v1_alt	132245
+chr8_KI270816v1_alt	305842
+chr8_KI270817v1_alt	158984
+chr8_KI270818v1_alt	145607
+chr8_KI270819v1_alt	133536
+chr8_KI270820v1_alt	36641
+chr8_KI270821v1_alt	985507
+chr8_KI270822v1_alt	624493
+chr8_KI270900v1_alt	318688
+chr8_KI270901v1_alt	136960
+chr8_KI270926v1_alt	229283
+chr8_KV880766v1_fix	156999
+chr8_KV880767v1_fix	265877
+chr8_KZ208914v1_fix	165121
+chr8_KZ208915v1_fix	6367529
+chr8_KZ559107v1_alt	103073
+chr8_MU273359v1_fix	150303
+chr8_MU273360v1_fix	39291
+chr8_MU273361v1_fix	106906
+chr8_MU273362v1_fix	429745
+chr8_MU273363v1_fix	207372
+chr9	138394718
+chr9_GL383539v1_alt	162989
+chr9_GL383540v1_alt	71552
+chr9_GL383541v1_alt	171287
+chr9_GL383542v1_alt	60033
+chr9_KI270717v1_random	40063
+chr9_KI270718v1_random	38055
+chr9_KI270719v1_random	176846
+chr9_KI270720v1_random	39051
+chr9_KI270823v1_alt	439083
+chr9_KN196479v1_fix	330165
+chr9_KQ090018v1_alt	163883
+chr9_KQ090019v1_alt	134100
+chr9_ML143353v1_fix	25409
+chr9_MU273364v1_fix	340718
+chr9_MU273365v1_fix	482251
+chr9_MU273366v1_fix	569669
+chrM	16570
+chrUn_GL000195v1	182897
+chrUn_GL000213v1	164240
+chrUn_GL000214v1	137719
+chrUn_GL000216v2	176609
+chrUn_GL000218v1	161148
+chrUn_GL000219v1	179199
+chrUn_GL000220v1	161803
+chrUn_GL000224v1	179694
+chrUn_GL000226v1	15009
+chrUn_KI270302v1	2275
+chrUn_KI270303v1	1943
+chrUn_KI270304v1	2166
+chrUn_KI270305v1	1473
+chrUn_KI270310v1	1202
+chrUn_KI270311v1	12400
+chrUn_KI270312v1	999
+chrUn_KI270315v1	2277
+chrUn_KI270316v1	1445
+chrUn_KI270317v1	37691
+chrUn_KI270320v1	4417
+chrUn_KI270322v1	21477
+chrUn_KI270329v1	1041
+chrUn_KI270330v1	1653
+chrUn_KI270333v1	2700
+chrUn_KI270334v1	1369
+chrUn_KI270335v1	1049
+chrUn_KI270336v1	1027
+chrUn_KI270337v1	1122
+chrUn_KI270338v1	1429
+chrUn_KI270340v1	1429
+chrUn_KI270362v1	3531
+chrUn_KI270363v1	1804
+chrUn_KI270364v1	2856
+chrUn_KI270366v1	8321
+chrUn_KI270371v1	2806
+chrUn_KI270372v1	1651
+chrUn_KI270373v1	1452
+chrUn_KI270374v1	2657
+chrUn_KI270375v1	2379
+chrUn_KI270376v1	1137
+chrUn_KI270378v1	1049
+chrUn_KI270379v1	1046
+chrUn_KI270381v1	1931
+chrUn_KI270382v1	4216
+chrUn_KI270383v1	1751
+chrUn_KI270384v1	1659
+chrUn_KI270385v1	991
+chrUn_KI270386v1	1789
+chrUn_KI270387v1	1538
+chrUn_KI270388v1	1217
+chrUn_KI270389v1	1299
+chrUn_KI270390v1	2388
+chrUn_KI270391v1	1485
+chrUn_KI270392v1	972
+chrUn_KI270393v1	1309
+chrUn_KI270394v1	971
+chrUn_KI270395v1	1144
+chrUn_KI270396v1	1881
+chrUn_KI270411v1	2647
+chrUn_KI270412v1	1180
+chrUn_KI270414v1	2490
+chrUn_KI270417v1	2044
+chrUn_KI270418v1	2146
+chrUn_KI270419v1	1030
+chrUn_KI270420v1	2322
+chrUn_KI270422v1	1446
+chrUn_KI270423v1	982
+chrUn_KI270424v1	2141
+chrUn_KI270425v1	1885
+chrUn_KI270429v1	1362
+chrUn_KI270435v1	92984
+chrUn_KI270438v1	112506
+chrUn_KI270442v1	392062
+chrUn_KI270448v1	7993
+chrUn_KI270465v1	1775
+chrUn_KI270466v1	1234
+chrUn_KI270467v1	3921
+chrUn_KI270468v1	4056
+chrUn_KI270507v1	5354
+chrUn_KI270508v1	1952
+chrUn_KI270509v1	2319
+chrUn_KI270510v1	2416
+chrUn_KI270511v1	8128
+chrUn_KI270512v1	22690
+chrUn_KI270515v1	6362
+chrUn_KI270516v1	1301
+chrUn_KI270517v1	3254
+chrUn_KI270518v1	2187
+chrUn_KI270519v1	138127
+chrUn_KI270521v1	7643
+chrUn_KI270522v1	5675
+chrUn_KI270528v1	2984
+chrUn_KI270529v1	1900
+chrUn_KI270530v1	2169
+chrUn_KI270538v1	91310
+chrUn_KI270539v1	994
+chrUn_KI270544v1	1203
+chrUn_KI270548v1	1600
+chrUn_KI270579v1	31034
+chrUn_KI270580v1	1554
+chrUn_KI270581v1	7047
+chrUn_KI270582v1	6505
+chrUn_KI270583v1	1401
+chrUn_KI270584v1	4514
+chrUn_KI270587v1	2970
+chrUn_KI270588v1	6159
+chrUn_KI270589v1	44475
+chrUn_KI270590v1	4686
+chrUn_KI270591v1	5797
+chrUn_KI270593v1	3042
+chrUn_KI270741v1	157433
+chrUn_KI270742v1	186740
+chrUn_KI270743v1	210659
+chrUn_KI270744v1	168473
+chrUn_KI270745v1	41892
+chrUn_KI270746v1	66487
+chrUn_KI270747v1	198736
+chrUn_KI270748v1	93322
+chrUn_KI270749v1	158760
+chrUn_KI270750v1	148851
+chrUn_KI270751v1	150743
+chrUn_KI270752v1	27746
+chrUn_KI270753v1	62945
+chrUn_KI270754v1	40192
+chrUn_KI270755v1	36724
+chrUn_KI270756v1	79591
+chrUn_KI270757v1	71252
+chrX	156040896
+chrX_KI270880v1_alt	284870
+chrX_KI270881v1_alt	144207
+chrX_KI270913v1_alt	274010
+chrX_KV766199v1_alt	188005
+chrX_ML143381v1_fix	403129
+chrX_ML143382v1_fix	28825
+chrX_ML143383v1_fix	68193
+chrX_ML143384v1_fix	14679
+chrX_ML143385v1_fix	17436
+chrX_MU273393v1_fix	68811
+chrX_MU273394v1_fix	140568
+chrX_MU273395v1_alt	619717
+chrX_MU273396v1_alt	294120
+chrX_MU273397v1_alt	330494
+chrY	57227416
+chrY_KI270740v1_random	37241
+chrY_KN196487v1_fix	101151
+chrY_KZ208923v1_fix	48371
+chrY_KZ208924v1_fix	209723
+chrY_MU273398v1_fix	865744
+CM000663.2	248956423
+CM000664.2	242193530
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diff --git a/nextflow/vcf_prepper/tests/testdata/homo_sapiens_core_110_38.dump b/nextflow/vcf_prepper/tests/testdata/homo_sapiens_core_110_38.dump
new file mode 100644
index 00000000..f54abe26
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/homo_sapiens_core_110_38.dump
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+/*!40000 ALTER TABLE `seq_region` ENABLE KEYS */;
+UNLOCK TABLES;
+
+
+--
+-- Table structure for table `seq_region_synonym`
+--
+
+DROP TABLE IF EXISTS `seq_region_synonym`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `seq_region_synonym` (
+  `seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `seq_region_id` int(10) unsigned NOT NULL,
+  `synonym` varchar(250) NOT NULL,
+  `external_db_id` int(10) unsigned DEFAULT NULL,
+  PRIMARY KEY (`seq_region_synonym_id`),
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=4717 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `seq_region_synonym`
+--
+
+LOCK TABLES `seq_region_synonym` WRITE;
+/*!40000 ALTER TABLE `seq_region_synonym` DISABLE KEYS */;
+INSERT INTO `seq_region_synonym` VALUES 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69,2006448172,'chr5_MU273353v1_fix',11000),(4670,2006448174,'chr5_MU273356v1_alt',11000),(4671,2006448176,'chr5_MU273355v1_fix',11000),(4672,2006448178,'chr5_MU273352v1_fix',11000),(4673,2006448180,'chr6_MU273357v1_alt',11000),(4674,2006448182,'chr7_MU273358v1_alt',11000),(4675,2006448184,'chr8_MU273362v1_fix',11000),(4676,2006448186,'chr8_MU273359v1_fix',11000),(4677,2006448188,'chr8_MU273361v1_fix',11000),(4678,2006448190,'chr8_MU273363v1_fix',11000),(4679,2006448192,'chr8_MU273360v1_fix',11000),(4680,2006448194,'chr9_MU273366v1_fix',11000),(4681,2006448196,'chr9_MU273364v1_fix',11000),(4682,2006448198,'chr9_MU273365v1_fix',11000),(4683,2006448200,'chr10_MU273367v1_fix',11000),(4684,2006448202,'chr11_KQ759759v2_fix',11000),(4685,2006448204,'chr11_MU273369v1_fix',11000),(4686,2006448206,'chr11_MU273371v1_fix',11000),(4687,2006448208,'chr11_MU273370v1_fix',11000),(4688,2006448210,'chr11_MU273368v1_alt',11000),(4689,2006448212,'chr12_MU273372v1_fix',11000),(4690,2006448214,'chr14_MU273373v1_fix',11000),(4691,2006448216,'chr15_MU273375v1_alt',11000),(4692,2006448218,'chr15_MU273374v1_fix',11000),(4693,2006448220,'chr16_MU273376v1_fix',11000),(4694,2006448222,'chr16_MU273377v1_fix',11000),(4695,2006448224,'chr17_MU273380v1_fix',11000),(4696,2006448226,'chr17_MU273378v1_alt',11000),(4697,2006448228,'chr17_MU273383v1_fix',11000),(4698,2006448230,'chr17_MU273379v1_fix',11000),(4699,2006448232,'chr17_MU273382v1_fix',11000),(4700,2006448234,'chr17_MU273381v1_fix',11000),(4701,2006448236,'chr19_MU273387v1_alt',11000),(4702,2006448238,'chr19_MU273384v1_fix',11000),(4703,2006448240,'chr19_MU273385v1_fix',11000),(4704,2006448242,'chr20_MU273388v1_fix',11000),(4705,2006448244,'chr20_MU273389v1_fix',11000),(4706,2006448246,'chr21_MU273390v1_fix',11000),(4707,2006448248,'chr21_MU273391v1_fix',11000),(4708,2006448250,'chr21_MU273392v1_fix',11000),(4709,2006448252,'chr22_KQ759762v2_fix',11000),(4710,2006448254,'chrX_MU273397v1_alt',11000),(4711,2006448256,'chrX_MU273393v1_fix',11000),(4712,2006448258,'chrX_MU273394v1_fix',11000),(4713,2006448260,'chrX_MU273396v1_alt',11000),(4714,2006448262,'chrX_MU273395v1_alt',11000),(4715,2006448264,'chrY_MU273398v1_fix',11000),(4716,131216,'na',1830);
+/*!40000 ALTER TABLE `seq_region_synonym` ENABLE KEYS */;
+UNLOCK TABLES;
+/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
+
+/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
+/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
+/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
+/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
+/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
+/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
+/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/data/homo_sapiens_grch38.synonyms b/nextflow/vcf_prepper/tests/testdata/homo_sapiens_grch38.synonyms
similarity index 100%
rename from nextflow/vcf_prepper/tests/data/homo_sapiens_grch38.synonyms
rename to nextflow/vcf_prepper/tests/testdata/homo_sapiens_grch38.synonyms
diff --git a/nextflow/vcf_prepper/tests/testdata/input_config.json b/nextflow/vcf_prepper/tests/testdata/input_config.json
new file mode 100644
index 00000000..4806d9f9
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/input_config.json
@@ -0,0 +1,12 @@
+{
+  "homo_sapiens_grch38": [
+    {
+      "genome_uuid": "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "source_name": "dbSNP",
+      "file_type": "local",
+      "file_location": "${BASE_DIR}/nextflow/vcf_prepper/tests/testdata/test.vcf.gz"
+    }
+  ]
+}
diff --git a/nextflow/vcf_prepper/tests/testdata/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz b/nextflow/vcf_prepper/tests/testdata/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
new file mode 100644
index 00000000..63a70c14
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz differ
diff --git a/nextflow/vcf_prepper/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz b/nextflow/vcf_prepper/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz
new file mode 100644
index 00000000..a984296b
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz differ
diff --git a/nextflow/vcf_prepper/tests/testdata/test.vcf.gz b/nextflow/vcf_prepper/tests/testdata/test.vcf.gz
new file mode 100644
index 00000000..85b451e5
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/test.vcf.gz differ
diff --git a/nextflow/vcf_prepper/tests/testdata/test.vcf.gz.csi b/nextflow/vcf_prepper/tests/testdata/test.vcf.gz.csi
new file mode 100644
index 00000000..7d231e73
Binary files /dev/null and b/nextflow/vcf_prepper/tests/testdata/test.vcf.gz.csi differ
diff --git a/nextflow/vcf_prepper/tests/testdata/test_db.ini b/nextflow/vcf_prepper/tests/testdata/test_db.ini
new file mode 100644
index 00000000..7b752739
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/test_db.ini
@@ -0,0 +1,9 @@
+[metadata]
+host = 127.0.0.1
+port = 3306
+user = root
+
+[core]
+host = 127.0.0.1
+port = 3306
+user = root
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/testdata/vep_config.json b/nextflow/vcf_prepper/tests/testdata/vep_config.json
new file mode 100644
index 00000000..360574c7
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/vep_config.json
@@ -0,0 +1,36 @@
+{
+    "annotation_source": {
+        "gff": {
+            "active": true
+        },
+        "fasta": {
+            "active": true
+        }
+    },
+    "default_options": {
+        "force_overwrite": 1,
+        "fork": 1,
+        "vcf": 1,
+        "spdi": 1,
+        "variant_class": 1,
+        "protein": 1,
+        "transcript_version": 1,
+        "gencode_promoter": 1
+    },
+    "plugins": {
+        "conf": [
+            {
+                "name": "CADD",
+                "keyed": true
+            },
+            {
+                "name": "SpliceAI",
+                "keyed": true
+            }
+        ]
+    },
+    "custom_annotaions": {
+        "conf": [
+        ]
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/tests/testdata/vep_config_missing_confs.json b/nextflow/vcf_prepper/tests/testdata/vep_config_missing_confs.json
new file mode 100644
index 00000000..951c583e
--- /dev/null
+++ b/nextflow/vcf_prepper/tests/testdata/vep_config_missing_confs.json
@@ -0,0 +1,20 @@
+{
+    "annotation_source": {
+        "gff": {
+            "active": true
+        },
+        "fasta": {
+            "active": true
+        }
+    },
+    "default_options": {
+        "force_overwrite": 1,
+        "fork": 1,
+        "vcf": 1,
+        "spdi": 1,
+        "variant_class": 1,
+        "protein": 1,
+        "transcript_version": 1,
+        "gencode_promoter": 1
+    }
+}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/workflows/vcf_prepper.nf b/nextflow/vcf_prepper/workflows/vcf_prepper.nf
deleted file mode 100755
index f725b64c..00000000
--- a/nextflow/vcf_prepper/workflows/vcf_prepper.nf
+++ /dev/null
@@ -1,204 +0,0 @@
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
- 
-//
-// Workflow to run Ensembl Variation vcf prepper Pipeline
-// The Goal of this workflow is to process and annotate VCF files and generate related track files for genome browser
-//
-
-import groovy.json.JsonSlurper
-import java.io.File
-
-def slurper = new JsonSlurper()
-params.config = slurper.parse(new File(params.input_config))
-
-include { CREATE_RANK_FILE } from "../modules/local/create_rank_file.nf"
-include { PREPARE_GENOME } from "../subworkflows/local/prepare_genome.nf"
-include { UPDATE_FIELDS } from "../modules/local/update_fields.nf"
-include { REMOVE_VARIANTS } from "../modules/local/remove_variants.nf"
-include { RUN_VEP } from "../subworkflows/local/run_vep.nf"
-include { COUNT_VCF_VARIANT } from "../modules/local/count_vcf_variant.nf"
-include { SPLIT_VCF } from "../subworkflows/local/split_vcf.nf"
-include { VCF_TO_BED } from "../modules/local/vcf_to_bed.nf"
-include { CONCAT_BEDS } from "../modules/local/concat_beds.nf"
-include { BED_TO_BIGBED } from "../modules/local/bed_to_bigbed.nf"
-include { BED_TO_WIG } from "../modules/local/bed_to_wig.nf"
-include { WIG_TO_BIGWIG } from "../modules/local/wig_to_bigwig.nf"
-include { SUMMARY_STATS } from "../modules/local/summary_stats.nf"
-
-def parse_config (config) {
-  input_set = []
-  
-  genomes = config.keySet()
-  for (genome in genomes) {
-    source_data = params.config.get(genome)
-    multiple_source = source_data.size() > 1 ? true : false
-    for (source_datum in source_data) {
-      vcf = source_datum.file_location
-      
-      meta = [:]
-      meta.genome = genome
-      meta.genome_uuid = source_datum.genome_uuid
-      meta.species = source_datum.species
-      meta.assembly = source_datum.assembly
-      meta.source = source_datum.source_name.replace(" ", "_")
-      meta.file_type = source_datum.file_type
-      meta.multiple_source = multiple_source
-
-      // replace whitespace and / character which causes issue in file name
-      meta.source = meta.source.replace(" ", "%20")
-      meta.source = meta.source.replace("/", "%2F")
-
-      // if source is MULTIPLE there are multiple sources; they must be listed  in sources field in the input config
-      if (meta.source == "MULTIPLE"){
-        meta.sources = source_data.sources.join(",")
-        meta.sources = meta.sources.replaceAll(" ", "%20") // we cannot use whitespace in cmd argument
-      }
-
-      meta.release_id = source_data.release_id ?: params.release_id
-      
-      input_set.add([meta, vcf])
-    }  
-  }
-  
-  return input_set
-}
-
-workflow VCF_PREPPER {
-  if (params.skip_vep && params.skip_tracks && params.skip_stats) {
-    exit 0, "Skipping VEP and track file generation, nothing to do ..."
-  }
-
-  if (params.use_old_infra && !params.use_vep_cache) {
-    exit 0, "Cannot use old infrastructure without VEP cache, please re-run with --use_vep_cache 1."
-  }
-  
-  input_set = parse_config(params.config)
-  ch_input = Channel.fromList( input_set )
-  
-  // setup
-  CREATE_RANK_FILE( params.rank_file )
-  PREPARE_GENOME( ch_input )
-    
-  // api files
-  if (!params.skip_vep) {
-    // pre-process
-    UPDATE_FIELDS( PREPARE_GENOME.out )
-    REMOVE_VARIANTS( UPDATE_FIELDS.out )
-    
-    // run vep
-    vep = RUN_VEP( REMOVE_VARIANTS.out )
-
-    // post-process
-    COUNT_VCF_VARIANT( vep )
-
-    COUNT_VCF_VARIANT.out
-    .map {
-      meta, vcf, vcf_index, variant_count ->
-        // if vcf has no variant - remove output directories and filter channel 
-        if ( variant_count.equals("0") ) {
-          file(meta.genome_api_outdir).delete()
-          file(meta.genome_tracks_outdir).delete()
-
-          "NO_VARIANT"
-        }
-        else {
-          [meta, vcf, vcf_index]
-        }
-    }
-    .filter { ! it.equals("NO_VARIANT") }
-    .set { ch_post_api }
-  }
-  else {
-    ch_post_api = PREPARE_GENOME.out
-  }
-
-  // track files
-  if (!params.skip_tracks) {
-    // create bed from VCF
-    // TODO: vcf_to_bed maybe faster without SPLIT_VCF - needs benchmarking
-    SPLIT_VCF( ch_post_api )
-    VCF_TO_BED( CREATE_RANK_FILE.out, SPLIT_VCF.out.transpose() )
-    CONCAT_BEDS( VCF_TO_BED.out.groupTuple() )
-
-    // create source tracks
-    // TODO: remove symlink creation for focus track when we have multiple source
-    BED_TO_BIGBED( CONCAT_BEDS.out )
-    BED_TO_WIG( CONCAT_BEDS.out )
-    WIG_TO_BIGWIG( BED_TO_WIG.out )
-
-    // if track generation is run vep-ed VCF file move needs to wait for this step to finish
-    SPLIT_VCF.out
-    .map {
-      meta, splits ->
-        [meta]
-    }
-    .set { ch_split_finish }
-  }
-
-  // summary stats
-  if (!params.skip_stats) {
-    // it can run in parallel to track generation
-    SUMMARY_STATS( ch_post_api )
-
-    SUMMARY_STATS.out
-    .set { ch_stats_finish }
-  }
-
-  // post process
-  if (!params.skip_vep || !params.skip_stats){
-    if(!params.skip_stats && !params.skip_tracks) {
-      ch_split_finish
-      .join ( ch_stats_finish )
-      .map {
-        meta, vcf, vcf_index ->
-          [meta, vcf, vcf_index]
-      }
-      .set { ch_post_process }
-    }
-    else if (params.skip_stats && !params.skip_tracks) {
-      ch_split_finish
-      .set { ch_post_process }
-    }
-    else if (!params.skip_stats && params.skip_tracks) {
-      ch_stats_finish
-      .set { ch_post_process }
-    }
-    else {
-      ch_post_api
-      .set { ch_post_process }
-    }
-
-    ch_post_process
-    .map {
-      meta, vcf, vcf_index ->
-        // TODO: when we have multiple source per genome we need to delete source specific files
-        new_vcf = meta.multiple_source ? 
-          "${meta.genome_api_outdir}/variation_${meta.source}.vcf.gz"
-          : "${meta.genome_api_outdir}/variation.vcf.gz"
-        new_vcf_index = "${new_vcf}.${meta.index_type}"
-        
-        // in -resume vcf and vcf_index may not exists as already renamed
-        // moveTo instead of renameTo - in -resume dest file may exists from previous run
-        if ( file(vcf).exists() && file(vcf_index).exists() ) {
-          file(vcf).moveTo(new_vcf)
-          file(vcf_index).moveTo(new_vcf_index)
-        }
-
-        [meta, new_vcf, new_vcf_index]
-    }
-  }
-}
diff --git a/nextflow/vcf_prepper/workflows/vcf_prepper/main.nf b/nextflow/vcf_prepper/workflows/vcf_prepper/main.nf
new file mode 100644
index 00000000..4ec82f2e
--- /dev/null
+++ b/nextflow/vcf_prepper/workflows/vcf_prepper/main.nf
@@ -0,0 +1,204 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+ 
+//
+// Workflow to run Ensembl Variation vcf prepper Pipeline
+// The Goal of this workflow is to process and annotate VCF files and generate related track files for genome browser
+//
+
+include { STAGE_FILE as STAGE_VCF } from "../../modules/local/stage_file"
+include { FORMAT_VCF } from "../../modules/local/format_vcf"
+include { GENERATE_VEP_CONFIG } from "../../subworkflows/local/generate_vep_config"
+include { RUN_VEP } from "../../subworkflows/local/run_vep"
+include { COUNT_VCF_VARIANT } from "../../modules/local/count_vcf_variant"
+include { CREATE_RANK_FILE } from "../../modules/local/create_rank_file"
+include { SPLIT_VCF } from "../../subworkflows/local/split_vcf"
+include { VCF_TO_BED } from "../../modules/local/vcf_to_bed"
+include { CONCAT_BEDS } from "../../modules/local/concat_beds"
+include { BED_TO_BIGBED } from "../../modules/local/bed_to_bigbed"
+include { BED_TO_WIG } from "../../modules/local/bed_to_wig"
+include { WIG_TO_BIGWIG } from "../../modules/local/wig_to_bigwig"
+include { SUMMARY_STATS as POST_FORMAT_VCF } from "../../modules/local/summary_stats"
+
+
+workflow VCF_PREPPER {
+	take:
+    ch_genome                       // channel: [ val(genome_meta) ]
+    ch_vcf                          // channel: [ val(genome_meta), val(file_meta), val(vcf) ]
+    fasta                           //     map: fasta meta map 
+    gff                             //     map: gff meta map
+    vep_cache                       //     map: cache meta map
+    default_options                 //     map: fasta meta map
+    vep_plugins                     //     map: fasta meta map
+    custom_annotations              //     map: fasta meta map
+    ch_synonym_file                 // channel: [ val(genome_meta), val(synonym_file) ]
+    ch_chrom_sizes_file             // channel: [ val(genome_meta), val(chrom_sizes_file ) ]
+    ini_file                        //     str: INI file with database connection info
+    structural_variant              //    bool: vcf contains structural variant?
+    version                         //     int: Ensembl (old) release version / schema version
+    release_id                      //     int: Ensembl release id
+    repo_dir                        //     str: path to Ensembl repositories
+    population_data_file            //     str: path to population_data.json
+    skip_vep                        //    bool: skip running VEP?
+    skip_tracks                     //.   bool: skip creating tracks?
+    skip_stats                      //    bool: skip adding summary stats?
+	bed_fields						// 	   str:	path to *_bedfields.json
+
+
+    main:
+    if (skip_vep && skip_tracks && skip_stats) {
+        error("Nothing to do...")
+    }
+  
+    // download/stage input VCF
+    STAGE_VCF( ch_vcf )
+    
+    // api files - run VEP annotation
+    if (!params.skip_vep) {
+        FORMAT_VCF( 
+            STAGE_VCF.out
+        )
+
+        GENERATE_VEP_CONFIG(
+            ch_genome,
+            fasta,
+            gff,
+            vep_cache,
+            default_options,
+            vep_plugins,
+            custom_annotations,
+            ini_file,
+            version,
+            release_id,
+            repo_dir,
+            population_data_file
+        )    
+              
+        RUN_VEP( 
+            FORMAT_VCF.out
+            .combine( GENERATE_VEP_CONFIG.out, by: 0 )
+        )
+
+		ch_post_vep = RUN_VEP.out
+	}
+    else {
+        ch_post_vep = STAGE_VCF.out
+    }
+        
+	// filter if no variant annotated from VEP
+	// it can happen, for example, when the input VCF has seq regions not present in VEP cache/gff/fasta
+	COUNT_VCF_VARIANT( ch_post_vep )
+	COUNT_VCF_VARIANT.out
+	.map {
+		genome_meta, file_meta, vcf, vcf_index, variant_count ->
+			// if vcf has no variant - remove output directories and filter channel 
+			if ( variant_count.equals("0") ) {
+				file(genome_meta.genome_api_outdir).delete()
+				file(genome_meta.genome_tracks_outdir).delete()
+
+				"NO_VARIANT"
+			}
+			else {
+				[genome_meta, file_meta, vcf, vcf_index]
+			}
+	}
+	.filter { ! it.equals("NO_VARIANT") }
+	.set { ch_filtered }
+
+	// summary stats/post format annotated VCF
+    if (!params.skip_stats) {
+        ch_post_stats = POST_FORMAT_VCF( 
+				ch_filtered,
+				population_data_file 
+			)
+    }
+    else {
+        ch_post_stats = ch_filtered
+    }
+
+    // track files
+    if (!params.skip_tracks) {
+        // create bed from VCF
+        // TODO: vcf_to_bed maybe faster without SPLIT_VCF - needs benchmarking
+        SPLIT_VCF( ch_filtered )
+        CREATE_RANK_FILE( params.rank_file )
+        VCF_TO_BED( 
+			SPLIT_VCF.out.transpose(),
+			CREATE_RANK_FILE.out,
+			bed_fields,
+			structural_variant
+		)
+        CONCAT_BEDS( VCF_TO_BED.out.groupTuple() )
+
+        // create source tracks
+        // TODO: remove symlink creation for focus track when we have multiple source
+        BED_TO_BIGBED( CONCAT_BEDS.out, bed_fields )
+        BED_TO_WIG( CONCAT_BEDS.out )
+        WIG_TO_BIGWIG( BED_TO_WIG.out )
+
+        // if track generation is run vep-ed VCF file move needs to wait for this step to finish
+        SPLIT_VCF.out
+        .map {
+        	meta, _splits ->
+            	[meta]
+        }
+        .set { ch_split_finish }
+    }
+
+  // post process
+  if (!params.skip_vep || !params.skip_stats){
+    if(!params.skip_stats && !params.skip_tracks) {
+      ch_split_finish
+      .join ( ch_post_stats )
+      .map {
+        genome_meta, file_meta, vcf, vcf_index ->
+          [genome_meta, file_meta, vcf, vcf_index]
+      }
+      .set { ch_post_process }
+    }
+    else if (params.skip_stats && !params.skip_tracks) {
+      ch_split_finish
+      .set { ch_post_process }
+    }
+    else if (!params.skip_stats && params.skip_tracks) {
+      ch_post_stats
+      .set { ch_post_process }
+    }
+    else {
+      ch_post_stats
+      .set { ch_post_process }
+    }
+
+    ch_post_process
+    .map {
+      genome_meta, file_meta, vcf, vcf_index ->
+        // TODO: when we have multiple source per genome we need to delete source specific files
+        def new_vcf = file_meta.multiple_source ? 
+          "${genome_meta.genome_api_outdir}/variation_${file_meta.source}.vcf.gz"
+          : "${genome_meta.genome_api_outdir}/variation.vcf.gz"
+        def new_vcf_index = "${new_vcf}.${genome_meta.index_type}"
+        
+        // in -resume vcf and vcf_index may not exists as already renamed
+        // moveTo instead of renameTo - in -resume dest file may exists from previous run
+        if ( file(vcf).exists() && file(vcf_index).exists() ) {
+          file(vcf).moveTo(new_vcf)
+          file(vcf_index).moveTo(new_vcf_index)
+        }
+
+        [genome_meta, file_meta, new_vcf, new_vcf_index]
+    }
+  }
+}
diff --git a/nextflow/vep_prepper/README.md b/nextflow/vep_prepper/README.md
index db0ff725..d36f9f23 100644
--- a/nextflow/vep_prepper/README.md
+++ b/nextflow/vep_prepper/README.md
@@ -5,7 +5,7 @@ nextflow run main.nf -profile slurm -base_dir BASE_DIR
 ```
 
 Params:
-    base_dir        : Base ftp directory. The pipeline will crawl the directory for gff and fasta file. Default: /hps/nobackup/flicek/ensembl/production/ensembl_dumps/ftp/organisms
+    base_dir        : Base ftp directory. The pipeline will crawl the directory for gff and fasta file. Default: null
     gff             : GFF file name. Pipeline will look for GFF file with this name. Default: genes.gff3.gz
     fasta           : FASTA file name. Pipeline will look for GFF file with this name. Default: unmasked.fa.gz
     outdir          : The directory where the processed file will be written.
diff --git a/nextflow/vep_prepper/workflows/vep_prepper.nf b/nextflow/vep_prepper/workflows/vep_prepper.nf
index b2286e31..ad331d7a 100755
--- a/nextflow/vep_prepper/workflows/vep_prepper.nf
+++ b/nextflow/vep_prepper/workflows/vep_prepper.nf
@@ -1,5 +1,5 @@
 // params used to crawl ftp directory to form input
-params.base_dir = "/hps/nobackup/flicek/ensembl/production/ensembl_dumps/ftp/organisms"
+params.base_dir = null // needs to be path to FTP base directory in /nfs
 params.fasta = "unmasked.fa.gz"
 params.gff = "genes.gff3.gz"
 
@@ -11,7 +11,7 @@ params.gff_file = ""
 params.fasta_file = ""
 
 // outdir_suffix can be used to create subdir under outdir for different genomes
-params.outdir = "/hps/nobackup/flicek/ensembl/variation/snhossain/website/vep_prepper/output"
+params.outdir = null
 params.outdir_suffix = ""
 
 // create payload? [TBD]
diff --git a/ruff.toml b/ruff.toml
index 19ee2e39..5a52506d 100644
--- a/ruff.toml
+++ b/ruff.toml
@@ -5,6 +5,9 @@
 line-length = 88 # Black style
 target-version = "py310"
 
+[lint]
+ignore = ["F403", "F405", "F401", "F541", "E722"]
+
 # --- Formatting ---
 [format]
 # Use double quotes everywhere (Black default)
diff --git a/src/python/LICENSE b/src/python/LICENSE
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/README.md b/src/python/README.md
new file mode 100644
index 00000000..36975d8e
--- /dev/null
+++ b/src/python/README.md
@@ -0,0 +1,66 @@
+# ensembl-variation-utils
+
+Python package for Ensembl Variation pipelines. Provides utilities for:
+
+- File location and management (FASTA, GFF, VEP cache, etc.)
+- Database access (metadata/core)
+- VEP config generation (JSON-based)
+- Specialized logic for VEP plugins and custom annotation data
+
+## Features
+
+- `clients`: Handles connections to metadata/core databases (future support for gRPC/REST)
+- `file_locator`: Discovers files and manages file operations
+- `vep_config`: Generates VEP configuration from JSON input
+
+## Usage
+
+Import the relevant modules in your pipeline scripts or Nextflow processes. Example:
+
+```python
+from ensembl.variation_utils.file_locator import FileLocator
+from ensembl.variation_utils.clients import MetadataClient
+from ensembl.variation_utils.vep_config import VEPConfig
+```
+
+See the [vcf_prepper pipeline](../../nextflow/vcf_prepper) for integration details.
+
+## Testing
+
+Unit tests are available in `tests/variation_utils/`.
+
+### Running tests locally
+
+#### 1. Install the package and test dependencies
+
+```bash
+pip install .
+pip install pytest coverage
+```
+
+#### 2. Set up test databases (optional)
+
+Some tests (e.g., `clients/`) require a local MySQL instance with test databases:
+
+```bash
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE ensembl_genome_metadata;'
+mysql -h 127.0.0.1 -u root ensembl_genome_metadata < tests/variation_utils/data/ensembl_genome_metadata.dump
+
+mysql -h 127.0.0.1 -u root -e 'CREATE DATABASE homo_sapiens_core_110_38;'
+mysql -h 127.0.0.1 -u root homo_sapiens_core_110_38 < tests/variation_utils/data/homo_sapiens_core_110_38.dump
+```
+
+#### 3. Run pytest
+
+```bash
+# Run all tests
+pytest .
+
+# Run with coverage
+coverage run -m pytest .
+coverage report
+```
+
+## License
+
+See LICENSE in this repository.
diff --git a/src/python/ensembl/variation_utils/__init__.py b/src/python/ensembl/variation_utils/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/ensembl/variation_utils/clients/clients.py b/src/python/ensembl/variation_utils/clients/clients.py
new file mode 100644
index 00000000..51417519
--- /dev/null
+++ b/src/python/ensembl/variation_utils/clients/clients.py
@@ -0,0 +1,143 @@
+from typing import Dict, List
+import configparser
+import subprocess
+
+# Database Client Classes
+class DBClient():
+    """Base database client"""
+    
+    def __init__(self, ini_file: str, section: str = "database"):
+        self._ini_file = ini_file
+        self._section = section
+
+        self._configure_server()
+
+    @property
+    def ini_file(self):
+        return self._ini_file
+    
+    @ini_file.setter
+    def ini_file(self, ini_file: str) -> str:
+        self._ini_file = ini_file
+        self._configure_server()
+
+        return self._ini_file
+    
+    @property
+    def section(self):
+        return self._section
+    
+    @section.setter
+    def section(self, section: str) -> str:
+        self._section = section
+        self._configure_server()
+
+        return self._section
+
+    def _configure_server(self) -> None:
+        server_config = self._parse_ini()
+        
+        self.host = server_config.get('host')
+        self.port = server_config.get('port')
+        self.user = server_config.get('user')
+        self.password = server_config.get('password')
+
+    def _parse_ini(self) -> Dict:
+        """Parse an ini file and return selected database connection parameters.
+
+        Args:
+            ini_file (str): Path to ini file.
+            section (str): Section name to read.
+
+        Returns:
+            list(dict): Mapping containing 'host', 'port' and 'user'.
+
+        Exits:
+            Exits the process if the requested section is not found.
+        """
+        ini_file = self.ini_file
+        section = self.section
+
+        config = configparser.ConfigParser()
+        config.read(ini_file)
+
+        server = {}
+        if section not in config:
+            raise Exception(f"[ERROR] Could not find {section} section in ini file - {ini_file}")
+        else:
+            server["host"] = config[section]["host"]
+            server["port"] = config[section]["port"]
+            server["user"] = config[section]["user"]
+            if "password" in config[section]:
+                server["password"] = config[section]["password"]
+
+        return server
+    
+    def run_query(self, query: str, dbname: str = None) -> str:
+        dbname_part = ""
+        if dbname is not None:
+            dbname_part = dbname
+
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                dbname_part,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        if (process.returncode != 0):
+            print("[WARNING] Query run failed")
+            print(
+                f"\tDatabase server - mysql://{self.user}:@{self.host}:{self.port}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+
+            return None
+        return process.stdout.decode().strip()
+    
+    # only for test
+    def load_sql(self, input_sql: str, dbname: str = None) -> str:
+        dbname_part = ""
+        if dbname is not None:
+            dbname_part = dbname
+
+        with open(input_sql) as file:
+            process = subprocess.run(
+                [
+                    "mysql",
+                    "--host", self.host,
+                    "--port", self.port,
+                    "--user", self.user,
+                    dbname_part,
+                    "-N"
+                ],
+                stdin=file,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+            print(process)
+            if (process.returncode != 0):
+                print("[WARNING] SQL loading failed")
+                print(
+                    f"\tDatabase server - mysql://{self.user}:@{self.host}:{self.port}"
+                )
+                print(f"\tError - {process.stderr.decode().strip()}")
+
+                return None
+
+            return process.stdout.decode().strip()
+        
+        return None
+    
+# gRPC Client Classes
+class GRPCClient():
+    """Base database client"""
+    pass
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/clients/core.py b/src/python/ensembl/variation_utils/clients/core.py
new file mode 100644
index 00000000..0309aae6
--- /dev/null
+++ b/src/python/ensembl/variation_utils/clients/core.py
@@ -0,0 +1,207 @@
+import subprocess
+from typing import Dict, List
+
+from . import clients
+
+class CoreDBClient(clients.DBClient):
+    """Core database client"""
+    
+    def __init__(self, ini_file: str, section: str = "core", dbname: str = None, species: str = None, version: str = None):
+        super().__init__(ini_file, section)
+        self.dbname = dbname
+        self._species = species
+        self._version = version
+
+        self._configure_server()
+        if dbname is None:
+            self._configure_db()
+
+    @property
+    def species(self):
+        return self._species
+    
+    @species.setter
+    def species(self, species: str) -> str:
+        self._species = species
+        self._configure_db()
+
+        return self._species
+    
+    @property
+    def version(self):
+        return self._version
+    
+    @version.setter
+    def version(self, version: str) -> str:
+        self._version = version
+        self._configure_db()
+
+        return self._version
+
+    def _configure_db(self) -> None:
+        """Return the first database name matching the species and version on the server.
+
+        Queries the MySQL server for databases matching the pattern and returns the
+        first match. A warning is printed if multiple matches are found.
+
+        Args:
+            species (str): Species production name.
+
+        Returns:
+            str: The first matching database name.
+        """
+        query = f"SHOW DATABASES LIKE '{self._species}_core%{self._version}%';"
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        results = process.stdout.decode().strip().split("\n")
+
+        if len(results) > 1:
+            print(
+                f"[WARNING] Multiple {type} database found, only first match is considered"
+            )
+
+        if results[0]:
+            self.dbname = results[0]
+
+    def update_db(self, species: str, version: str) -> None:
+        self._species = species
+        self._version = version
+        self._configure_db()
+
+    def run_query(self, query):
+        return super().run_query(query, dbname=self.dbname)
+
+    def get_meta_value(self, meta_key: str) -> str:
+        query = f"SELECT meta_value FROM meta WHERE meta_key = '{meta_key}';"
+
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        if (process.returncode != 0):
+            print(f"[WARNING] Could not get {meta_key} from core database - {self.dbname}")
+            print(
+                f"\tDatabase server - mysql://{self.user}:@{self.host}:{self.port}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+
+            return None
+        return process.stdout.decode().strip()
+    
+    def get_schema_version(self) -> str:
+        return self.get_meta_value("schema_version")
+
+    def get_species_production_name(self) -> str:
+        return self.get_meta_value("species.production_name")
+
+    def get_species_url(self) -> str:
+        return self.get_meta_value("species.url")
+
+    def get_assembly_default(self) -> str:
+        return self.get_meta_value("assembly.default")
+    
+    def get_division(self) -> str:
+        """Return the Ensembl division for a given core database.
+
+        Returns:
+            str: Division name (one of known Ensembl divisions).
+
+        Exits:
+            Exits the process with an error message if division cannot be determined.
+        """
+        # TMP: this is only temp as ensemblgenome FTP had problem in 110
+        if self.dbname.startswith("drosophila_melanogaster"):
+            return "EnsemblVertebrates"
+        division = self.get_meta_value("species.division")
+
+        ensembl_divisions = [
+            "EnsemblVertebrates",
+            "EnsemblFungi",
+            "EnsemblMetazoa",
+            "EnsemblPlants",
+            "EnsemblProtists",
+        ]
+        if ( division not in ensembl_divisions):
+            print(f"[WARNING] Invalid ensembl division - {division}")
+            return None
+        
+        return division
+    
+    def get_coord_id_by_version(self, version: str) -> str:
+        query = f"SELECT coord_system_id FROM coord_system WHERE version = '{version}';"
+
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        if (process.returncode != 0):
+            print(f"[WARNING] Could not get coord_id for version - {version}")
+            print(
+                f"\tDatabase server - mysql://{self.user}:@{self.host}:{self.port}/{self.dbname}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+
+            return None
+        return process.stdout.decode().strip()
+    
+    def get_coord_id_by_version(self, version: str) -> str:
+        query = f"SELECT coord_system_id FROM coord_system WHERE version = '{version}';"
+
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        if (process.returncode != 0):
+            print(f"[WARNING] Could not get coord_id for version - {version}")
+            print(
+                f"\tDatabase server - mysql://{self.user}:@{self.host}:{self.port}/{self.dbname}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+
+            return None
+        return process.stdout.decode().strip()
+    
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/clients/metadata.py b/src/python/ensembl/variation_utils/clients/metadata.py
new file mode 100644
index 00000000..5300f6d8
--- /dev/null
+++ b/src/python/ensembl/variation_utils/clients/metadata.py
@@ -0,0 +1,219 @@
+from abc import ABC, abstractmethod
+import subprocess
+
+from . import clients
+
+class MetadataClient(ABC):
+    """Abstract base class for metadata clients"""
+    
+    @abstractmethod
+    def get_assembly_accession(self, genome_uuid: str) -> str:
+        """Get assembly accession for a genome UUID"""
+        pass
+    
+    @abstractmethod
+    def get_scientific_name(self, genome_uuid: str) -> str:
+        """Get scientific name for a genome UUID"""
+        pass
+    
+    @abstractmethod
+    def get_dataset_uuid(self, genome_uuid: str, dataset_type: str, release_id: int = None) -> str:
+        """Get dataset UUID"""
+        pass
+    
+    @abstractmethod
+    def get_dataset_attribute_value(self, dataset_uuid: str, attrib_name: str) -> str:
+        """Get dataset attribute value"""
+        pass
+
+class MetadataDBClient(clients.DBClient, MetadataClient):
+    """Database-based metadata client"""
+    
+    def __init__(self, ini_file: str, section:str = "metadata", dbname: str = "ensembl_genome_metadata"):
+        super().__init__(ini_file=ini_file, section=section)
+        self.dbname = dbname
+    
+    def get_scientific_name(self, genome_uuid: str) -> str:
+        """Retrieve the scientific name of a species from metadata DB.
+
+        Args:
+            genome_uuid (str): Genome UUID.
+
+        Returns:
+            str|None: Scientific name, or None if retrieval failed.
+        """
+        query = (
+            "SELECT o.scientific_name"
+            + " FROM genome g"
+            + " JOIN organism o on o.organism_id = g.organism_id"
+            + f" WHERE g.genome_uuid = '{genome_uuid}';"
+        )
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        if process.returncode != 0:
+            print(
+                f"[WARNING] Failed to retrieve species scientific name for genome - {genome_uuid}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+            return None
+
+        return process.stdout.decode().strip()
+
+    def get_assembly_accession(self, genome_uuid: str) -> str:
+        """Retrieve assembly accession for a genome UUID from metadata DB.
+
+        Args:
+            genome_uuid (str): Genome UUID.
+
+        Returns:
+            str: Assembly accession string (empty if not found).
+        """
+        query = f"SELECT a.accession FROM assembly AS a, genome AS g WHERE g.assembly_id = a.assembly_id AND g.genome_uuid = '{genome_uuid}';"
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+
+        return process.stdout.decode().strip()
+
+    def get_dataset_uuid(self, genome_uuid: str, dataset_type: str, release_id: int = None) -> str:
+        """Retrieve a dataset attribute value for a genome and release.
+
+        Args:
+            genome_uuid (str): dataset UUID.
+            dataset_type (str): dataset type.
+            release_id (int): release id.
+
+        Returns:
+            str|None: dataset UUID or None on failure.
+        """
+        release_clause = f" AND gd.release_id = {release_id}"
+        if release_id is None:
+            release_clause = " AND gd.is_current = 1"
+
+        query = (
+            "SELECT DISTINCT d.dataset_uuid FROM genome g"
+            + " JOIN genome_dataset gd on g.genome_id = gd.genome_id"
+            + " JOIN dataset d on gd.dataset_id = d.dataset_id"
+            + " JOIN dataset_type dt on d.dataset_type_id = dt.dataset_type_id"
+            + " JOIN dataset_attribute da on d.dataset_id = da.dataset_id"
+            + f" WHERE g.genome_uuid = '{genome_uuid}'"
+            + f" AND dt.name = '{dataset_type}'"
+            + release_clause + ";"
+        )
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        print(process)
+        if process.returncode != 0:
+            print(
+                f"[WARNING] Failed to retrieve dataset uuid for genome {genome_uuid}, dataset type - {dataset_type}, and release - {release_id}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+            return None
+
+        return process.stdout.decode().strip()
+
+    
+    def get_dataset_attribute_value(self, dataset_uuid: str, attrib_name: str) -> str:
+        """Retrieve a dataset attribute value for a genome and release.
+
+        Args:
+            dataset_uuid (str): dataset UUID.
+            attrib_name (str): Attribute name to retrieve.
+
+        Returns:
+            str|None: Attribute value or None on failure.
+        """
+        query = (
+            "SELECT da.value FROM dataset d"
+            + " JOIN dataset_attribute da on d.dataset_id = da.dataset_id"
+            + " JOIN attribute a on da.attribute_id = a.attribute_id"
+            + f" WHERE d.dataset_uuid = '{dataset_uuid}'"
+            + f" AND a.name = '{attrib_name}';"
+        )
+        process = subprocess.run(
+            [
+                "mysql",
+                "--host", self.host,
+                "--port", self.port,
+                "--user", self.user,
+                "--database", self.dbname,
+                "-N",
+                "--execute",
+                query,
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        if process.returncode != 0:
+            print(
+                f"[WARNING] Failed to retrieve {attrib_name} dataset attribute for dataset - {dataset_uuid}"
+            )
+            print(f"\tError - {process.stderr.decode().strip()}")
+            return None
+
+        return process.stdout.decode().strip()
+
+
+class MetadataGRPCClient(clients.GRPCClient, MetadataClient):
+    """gRPC-based metadata client"""
+    
+    def configure(self) -> None:
+        """Configure gRPC connection"""
+        # Implementation would establish gRPC connection
+        pass
+    
+    def get_assembly_accession(self, genome_uuid: str) -> str:
+        """Get assembly accession via gRPC"""
+        # Implementation would call gRPC service
+        pass
+    
+    def get_scientific_name(self, genome_uuid: str) -> str:
+        """Get scientific name via gRPC"""
+        # Implementation would call gRPC service
+        pass
+    
+    def get_dataset_uuid(self, genome_uuid: str, dataset_type: str, release_id: int) -> str:
+        """Get dataset UUID via gRPC"""
+        # Implementation would call gRPC service
+        pass
+    
+    def get_dataset_attribute_value(self, dataset_uuid: str, attrib_name: str) -> str:
+        """Get dataset attribute value via gRPC"""
+        # Implementation would call gRPC service
+        pass
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_locator/fasta.py b/src/python/ensembl/variation_utils/file_locator/fasta.py
new file mode 100644
index 00000000..b2401bb4
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/fasta.py
@@ -0,0 +1,79 @@
+import os
+
+from . import file_locator
+from . import ftp
+
+class FASTALocatorFactory(file_locator.FileLocatorFactory):
+    """Locator for FASTA files"""
+    
+    def __init__(self):
+        super().__init__()
+        self.locator: file_locator.FileLocator = None
+
+    @property
+    def locator(self):
+        return self._locator
+    
+    @locator.setter
+    def locator(self, locator: file_locator.FileLocator) -> file_locator.FileLocator:
+        self._locator = locator
+        return self._locator
+    
+    def set_locator(
+                self, 
+                type: ftp.InfrastructureType = ftp.InfrastructureType.CURRENT.value
+            ) -> file_locator.FileLocator:
+        """Set the underlying file locator based on infrastructure type"""
+        if type == ftp.InfrastructureType.CURRENT.value:
+            self.locator = FTPFASTALocator()
+        elif type == ftp.InfrastructureType.OLD.value:
+            self.locator = OldFTPFASTALocator()
+        else:
+            raise Exception(f"[WARNING] Not a supported factory type - {type}")
+        return self.locator
+
+class FTPFASTALocator(ftp.FTPFileLocator):
+    """FTP-specific FASTA file locator"""
+    
+    def locate_file(self, genome_uuid: str) -> str:
+        """Locate FASTA file for specific genome"""
+        species_name = self.get_species_name(genome_uuid)
+        assembly = self.get_assembly(genome_uuid)
+        
+        # Construct file path based on metadata
+        relative_path = os.path.join(
+            species_name,
+            assembly,
+            "genome",
+        )
+        file_name = "unmasked.fa.gz"
+
+        self.file = os.path.join(self.base_path, relative_path, file_name)
+        return self.file
+
+class OldFTPFASTALocator(ftp.OldFTPFileLocator):
+    """Old FTP FASTA file locator"""
+    
+    def __init__(self):
+        super().__init__()
+    
+    def locate_file(self) -> str:
+        """Locate FASTA file using old structure"""
+        version = self.get_version()
+        division = self.get_division_segment()
+        species_url = self._core_db_client.get_species_url()
+        species_production_name = self._core_db_client.get_species_production_name()
+        assembly = self._assembly
+        
+        # Construct file path based on metadata
+        relative_path = os.path.join(
+            f"release-{version}",
+            division,
+            "fasta",
+            species_production_name,
+            "dna"
+        )
+        file_name = f"{species_url}.{assembly}.dna.toplevel.fa.gz"
+        
+        self.file = os.path.join(self.base_path, relative_path, file_name)
+        return self.file
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_locator/file_locator.py b/src/python/ensembl/variation_utils/file_locator/file_locator.py
new file mode 100644
index 00000000..d605b622
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/file_locator.py
@@ -0,0 +1,26 @@
+from abc import ABC, abstractmethod
+from typing import Optional
+
+class FileLocator(ABC):
+    """Abstract base class for file locators"""
+    
+    def __init__(self):
+        self.file: Optional[str] = None
+    
+    @abstractmethod
+    def locate_file(self) -> str:
+        """Locate a file and return its path"""
+        pass
+    
+    @abstractmethod
+    def copy_file(self, target_dir: str) -> bool:
+        """Copy file to target directory"""
+        pass  
+
+# Factory Classes
+class FileLocatorFactory(ABC):
+    """Factory for creating file locators"""
+
+    @abstractmethod
+    def set_locator(self):
+        pass
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_locator/ftp.py b/src/python/ensembl/variation_utils/file_locator/ftp.py
new file mode 100644
index 00000000..9a0ec5ff
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/ftp.py
@@ -0,0 +1,174 @@
+import shutil
+import os
+import re
+from enum import Enum
+
+from . import file_locator
+from . import utils
+from ..clients import core, metadata
+
+class InfrastructureType(Enum):
+    OLD = "old"
+    CURRENT = "current"
+
+class StorageMediaType(Enum):
+    DISK = "disk"
+    SERVER = "server"
+
+class FTPFileLocator(file_locator.FileLocator):
+    BASE_PATH = {
+        StorageMediaType.DISK: os.environ["FTP_NFS_DIR"],
+        StorageMediaType.SERVER: "https://ftp.ebi.ac.uk/pub/ensemblorganisms"
+    }
+
+    def __init__(
+            self,
+            metadata_client: metadata.MetadataClient = None,
+            storage_media: StorageMediaType = StorageMediaType.DISK
+        ):
+        super().__init__()
+        self.metadata_client = metadata_client
+        self.storage_media = storage_media 
+
+    @property
+    def storage_media(self):
+        return self._storage_media
+    
+    @storage_media.setter
+    def storage_media(self, storage_media: StorageMediaType):
+        self._storage_media = storage_media
+        self.base_path = self.BASE_PATH[storage_media]
+
+        return self._storage_media
+
+    def locate_file(self, relative_path: str) -> str:
+        self.file = os.path.join(self.base_path, relative_path)
+        return self.file
+    
+    def copy_file(self, target_file: str) -> bool:
+        if (self.storage_media == StorageMediaType.DISK):
+            return utils.copy_file(self.file, target_file)
+        elif (self.storage_media == StorageMediaType.SERVER):
+            return utils.download_file(self.file, target_file)
+    
+    def get_species_name(self, genome_uuid: str) -> str:
+        scientific_name = self.metadata_client.get_scientific_name(genome_uuid)
+        if scientific_name == "" or scientific_name is None:
+            raise Exception(
+                f"[ERROR] Could not retrieve scientific name for genome uuid - {genome_uuid}"
+            )
+        scientific_name = scientific_name.replace(" ", "_")
+        scientific_name = re.sub("[^a-zA-Z0-9]+", " ", scientific_name)
+        scientific_name = re.sub(" +", "_", scientific_name)
+        scientific_name = re.sub("^_+|_+$", "", scientific_name)
+        
+        return scientific_name
+    
+    def get_assembly(self, genome_uuid: str) -> str:
+        assembly_accession = self.metadata_client.get_assembly_accession(genome_uuid)
+        if assembly_accession == "" or assembly_accession is None:
+            raise Exception(
+                f"[ERROR] Could not retrieve assembly accession for genome uuid - {genome_uuid}"
+            )
+        
+        return assembly_accession
+
+# Old FTP File Locators (for backward compatibility)
+class OldFTPFileLocator(file_locator.FileLocator):
+
+    def __init__(
+                self,
+                core_db_client: core.CoreDBClient = None,
+                storage_media: StorageMediaType = StorageMediaType.DISK
+            ):
+        self._division = "EnsemblVertebrates" 
+        self._assembly = "GRCh38"
+        self._core_db_client = core_db_client
+        self._storage_media = storage_media
+
+        self._set_base_path()
+    
+    @property
+    def core_db_client(self):
+        return self._core_db_client
+    
+    @core_db_client.setter
+    def core_db_client(self, core_db_client: core.CoreDBClient):
+        self._core_db_client = core_db_client
+        self._division = core_db_client.get_division()
+        self._assembly = core_db_client.get_assembly_default()
+        self._set_base_path()
+
+        return self._core_db_client
+
+    @property
+    def storage_media(self):
+        return self._storage_media
+    
+    @storage_media.setter
+    def storage_media(self, storage_media: StorageMediaType):
+        self._storage_media = storage_media
+        self._set_base_path()
+
+        return self._storage_media
+    
+    @property
+    def division(self):
+        return self._division
+    
+    @division.setter
+    def division(self, division: str):
+        self._division = division
+        self._set_base_path()
+
+        return self._division
+    
+    @property
+    def assembly(self):
+        return self._assembly
+    
+    @assembly.setter
+    def assembly(self, assembly: str):
+        self._assembly = assembly
+        self._set_base_path()
+
+        return self._assembly
+
+    def _set_base_path(self):
+        if self._storage_media == StorageMediaType.DISK:
+            # REMOVE THIS!! "/nfs/production/flicek/ensembl/production/ensemblftp"
+            self.base_path = os.environ["OLD_FTP_NFS_DIR"]
+        elif self._storage_media == StorageMediaType.SERVER:
+            if self._division == "EnsemblVertebrates":
+                if self._assembly == "GRCh37":
+                    self.base_path = "https://ftp.ensembl.org/pub/grch37"
+                else:
+                    self.base_path = "https://ftp.ensembl.org/pub"
+            else:
+                self.base_path = "https://ftp.ensemblgenomes.org/pub"
+
+    def locate_file(self, relative_path: str) -> str:
+        self.file = os.path.join(self.base_path, relative_path)
+        return self.file
+    
+    def copy_file(self, target_file: str) -> bool:
+        if (self.storage_media == StorageMediaType.DISK):
+            return utils.copy_file(self.file, target_file)
+        elif (self.storage_media == StorageMediaType.SERVER):
+            return utils.download_file(self.file, target_file)
+    
+    def get_division_segment(self):
+        if self._division == "EnsemblVertebrates":
+            return ""
+        else:
+            return f"{self._division[7:].lower()}"
+        
+    def get_version(self) -> int:
+        if self._core_db_client is None:
+            raise Exception("[ERROR] Cannot get version without a core db client")
+        
+        schema_version = self._core_db_client.get_schema_version()
+        if self._division == "EnsemblVertebrates":
+            return schema_version
+        else:
+            return str(int(schema_version) - 53)
diff --git a/src/python/ensembl/variation_utils/file_locator/gff.py b/src/python/ensembl/variation_utils/file_locator/gff.py
new file mode 100644
index 00000000..2517706c
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/gff.py
@@ -0,0 +1,77 @@
+import re
+import os
+from enum import Enum
+
+from . import file_locator
+from . import ftp
+
+# Specific File Type Locators
+class GFFLocatorFactory(file_locator.FileLocatorFactory):
+    """Locator for GFF files"""
+    
+    def __init__(self):
+        super().__init__()
+        self._locator: file_locator.FileLocator = None
+
+    @property
+    def locator(self):
+        return self._locator
+
+    @locator.setter
+    def locator(self, locator: file_locator.FileLocator) -> file_locator.FileLocator:
+        self._locator = locator
+        return self._locator
+    
+    def set_locator(
+            self, 
+            type: ftp.InfrastructureType = ftp.InfrastructureType.CURRENT.value
+        ) -> file_locator.FileLocator:
+        """Set the underlying file locator based on infrastructure type"""
+        if type == ftp.InfrastructureType.CURRENT.value:
+            self.locator = FTPGFFLocator()
+        else:
+            raise Exception(f"[WARNING] Not a supported factory type - {type}")
+        return self.locator
+
+class FTPGFFLocator(ftp.FTPFileLocator):
+    """FTP-specific GFF file locator"""
+    
+    def locate_file(self, genome_uuid: str) -> str:
+        """Locate GFF file for specific genome and annotation source"""
+        species_name = self.get_species_name(genome_uuid)
+        assembly = self.get_assembly(genome_uuid)
+        
+        dataset_uuid = self.metadata_client.get_dataset_uuid(genome_uuid, dataset_type="genebuild")
+        annotation_source = self.metadata_client.get_dataset_attribute_value(
+            dataset_uuid, 
+            attrib_name="genebuild.annotation_source"
+        )
+        if annotation_source == "" or annotation_source is None:
+            raise Exception(
+                f"[ERROR] Could not retrieve genebuild annotation source for dataset uuid - {dataset_uuid}"
+            )
+        annotation_source = annotation_source.lower()
+        
+        last_geneset_update = self.metadata_client.get_dataset_attribute_value(
+            dataset_uuid, 
+            attrib_name="genebuild.last_geneset_update"
+        )
+        if last_geneset_update == "" or last_geneset_update is None:
+            raise Exception(
+                f"[ERROR] Could not retrieve last genebuild udpate date for genome uuid - {dataset_uuid}"
+            )
+        last_geneset_update = last_geneset_update.replace("-", "_")
+        last_geneset_update = re.sub("[\-\s]", "_", last_geneset_update)
+        
+        # Construct file path based on metadata
+        relative_path = os.path.join(
+            species_name,
+            assembly,
+            annotation_source,
+            "geneset",
+            last_geneset_update
+        )
+        file_name = "genes.gff3.gz"
+
+        self.file =  os.path.join(self.base_path, relative_path, file_name)
+        return self.file
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_locator/utils.py b/src/python/ensembl/variation_utils/file_locator/utils.py
new file mode 100644
index 00000000..d5abfac8
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/utils.py
@@ -0,0 +1,42 @@
+import os
+import shutil
+import subprocess
+
+
+def download_file(url: str, target_file: str) -> bool:
+    """Download a remote file using wget.
+
+    Args:
+        url (str): Remote URL to download.
+        target_dir (str): Target directory to write.
+
+    Returns:
+        int: Return code from the wget subprocess; non-zero indicates failure.
+    """
+    process = subprocess.run(
+        ["wget", url, "-O", target_file],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+
+    if process.returncode != 0:
+        print(
+            f"[WARNING] Failed to download - {url}"
+            + f"\tError = {process.stderr}"
+        )
+        if os.path.isfile(target_file):
+            os.remove(target_file)
+
+    return process.returncode == 0
+
+def copy_file(source_file, target_file) -> bool:
+    try:
+        shutil.copy(source_file, target_file)
+        return True
+    except Exception as e:
+        print(
+            f"[WARNING] Copy failed - {e}\n"
+            + f"\tsource file - {source_file}\n"
+            + f"\ttarget directory - {target_file}"
+        )
+        return False
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_locator/vep_cache.py b/src/python/ensembl/variation_utils/file_locator/vep_cache.py
new file mode 100644
index 00000000..079095d3
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_locator/vep_cache.py
@@ -0,0 +1,51 @@
+import os
+
+from . import file_locator
+from . import ftp
+
+class VEPCacheLocatorFactory(file_locator.FileLocatorFactory):
+    """Locator for FASTA files"""
+    
+    def __init__(self):
+        super().__init__()
+        self._locator: file_locator.FileLocator = None
+
+    @property
+    def locator(self):
+        return self._locator
+    
+    def set_locator(
+                self, 
+                type: ftp.InfrastructureType = ftp.InfrastructureType.OLD.value
+            ) -> file_locator.FileLocator:
+        """Set the underlying file locator based on infrastructure type"""
+        if type == ftp.InfrastructureType.OLD.value:
+            self._locator = OldFTPVEPCahceLocator()
+        else:
+            raise Exception(f"[WARNING] Not a supported factory type - {type}")
+        return self._locator
+
+class OldFTPVEPCahceLocator(ftp.OldFTPFileLocator):
+    """Old FTP FASTA file locator"""
+    
+    def __init__(self):
+        super().__init__()
+    
+    def locate_file(self) -> str:
+        """Locate FASTA file using old structure"""
+        version = self.get_version()
+        division = self.get_division_segment()
+        species_production_name = self._core_db_client.get_species_production_name()
+        assembly = self._assembly
+        
+        # Construct file path based on metadata
+        relative_path = os.path.join(
+            f"release-{version}",
+            division,
+            "variation",
+            "indexed_vep_cache"
+        )
+        file_name = f"{species_production_name}_vep_{version}_{assembly}.tar.gz"
+        
+        self.file = os.path.join(self.base_path, relative_path, file_name)
+        return self.file
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/file_utils.py b/src/python/ensembl/variation_utils/file_utils.py
new file mode 100644
index 00000000..8c8cf5b7
--- /dev/null
+++ b/src/python/ensembl/variation_utils/file_utils.py
@@ -0,0 +1,63 @@
+import os
+import subprocess
+
+def is_bgzip(file: str) -> bool:
+    with open(file, "rb") as f:
+        gzip = (f.read(2) == b'\x1f\x8b')
+        f.seek(12)
+        bgzip_extra_field = (f.read(2) == b'BC')
+
+        return gzip and bgzip_extra_field
+    
+def ungzip_file(file: str) -> str:
+    """Decompress a gzip file in place and return the decompressed filename.
+
+    Args:
+        file (str): Path to the .gz file.
+
+    Returns:
+        str: Decompressed filename (original minus '.gz').
+
+    Raises:
+        FileNotFoundError: If the input file does not exist.
+        SystemExit: Exits with an error if gzip fails.
+    """
+    if not os.path.isfile(file):
+        raise FileNotFoundError(f"Could not un-gzip. File does not exist - {file}")
+
+    process = subprocess.run(
+        ["gzip", "-df", file], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+    )
+
+    if process.returncode != 0:
+        print(f"[ERROR] Could not uncompress file - {file}")
+        exit(1)
+
+    return file[:-3]
+
+
+def bgzip_file(file: str) -> str:
+    """Compress a file using bgzip and return the compressed filename.
+
+    Args:
+        file (str): Path to a file to compress.
+
+    Returns:
+        str: Path to the compressed file (appended with '.gz').
+
+    Raises:
+        FileNotFoundError: If the input file does not exist.
+        SystemExit: Exits with an error if bgzip fails.
+    """
+    if not os.path.isfile(file):
+        raise FileNotFoundError(f"Could not run bgzip. File does not exist - {file}")
+
+    process = subprocess.run(
+        ["bgzip", "-f", file], stdout=subprocess.PIPE, stderr=subprocess.PIPE
+    )
+
+    if process.returncode != 0:
+        print(f"[ERROR] Could not bgzip file - {file}")
+        exit(1)
+
+    return file + ".gz"
diff --git a/src/python/ensembl/variation_utils/vep_config/custom_annotation.py b/src/python/ensembl/variation_utils/vep_config/custom_annotation.py
new file mode 100644
index 00000000..3af32a5f
--- /dev/null
+++ b/src/python/ensembl/variation_utils/vep_config/custom_annotation.py
@@ -0,0 +1,88 @@
+from abc import ABC, abstractmethod
+from typing import List
+import json
+import re
+
+class CustomAnnotationArgsBuilder(ABC):
+    @abstractmethod
+    def match(self):
+        pass
+
+    @abstractmethod
+    def get_args(self):
+        pass
+    
+class FrequencyArgsBuilderFactory():
+    def __init__(self):
+        self._builder: CustomAnnotationArgsBuilder = None
+
+    def set_builder(self, type: str = "CURRENT") -> CustomAnnotationArgsBuilder:
+        if type == "CURRENT":
+            self._builder = PopulationDataConfigBuilder()
+        return self._builder
+
+class PopulationDataConfigBuilder(CustomAnnotationArgsBuilder):
+    def __init__(
+                self,
+                population_data_file: str = None,
+                species: str = None,
+                assembly_accession: str = None
+            ) -> None:
+        self.population_data_file = population_data_file
+        self.species = species
+        self.assembly_accession = assembly_accession
+
+    @property
+    def population_data_file(self):
+        return self._population_data_file
+    
+    @population_data_file.setter
+    def population_data_file(self, population_data_file: str) -> str:
+        self._population_data_file = population_data_file
+
+        if population_data_file is not None:
+            with open(self._population_data_file, "r") as file:
+                self._population_data = json.load(file)
+
+        return self._population_data_file
+
+    def match(self) -> bool:
+        """Set the underlying file locator based on infrastructure type"""
+        for species_pattern in self._population_data:
+            if re.fullmatch(species_pattern, self.species):
+                self.species_pattern = species_pattern
+                return True
+        return False
+    
+    def get_args(self) -> List:
+        populations = self._population_data[self.species_pattern]
+
+        args = []
+        for population in populations:
+            for file in population["files"]:
+                short_name = file["short_name"]
+                file_location = file["file_location"]
+                fields = [
+                    field
+                    for pop in file["include_fields"]
+                    for field in list(pop["fields"].values())
+                ]
+
+                if "##ASSEMBLY_ACC##" in file_location:
+                    if self._assembly is None:
+                        print(f"[WARNING] Cannot replace ##ASSEMBLY_ACC## in {short_name} population file path")
+                        continue
+
+                    file_location = file_location.replace(
+                            "##ASSEMBLY_ACC##", 
+                            self._assembly
+                        )
+
+                args.append({
+                    "short_name": short_name,
+                    "file": file_location,
+                    "format": "vcf",
+                    "fields": fields
+                })
+
+        return args
\ No newline at end of file
diff --git a/src/python/ensembl/variation_utils/vep_config/plugin.py b/src/python/ensembl/variation_utils/vep_config/plugin.py
new file mode 100644
index 00000000..0647f4e6
--- /dev/null
+++ b/src/python/ensembl/variation_utils/vep_config/plugin.py
@@ -0,0 +1,275 @@
+from typing import List, Dict
+import json
+import os
+import subprocess
+from abc import ABC, abstractmethod
+
+#
+# Plugin Matchers
+#
+class PluginArgsBuilder(ABC):
+    @abstractmethod
+    def match(self) -> bool:
+        pass
+
+    def get_args(self) -> str:
+        pass
+
+class PluginArgsBuilderFactory():
+    def __init__(self):
+        self._builder: PluginArgsBuilder = None
+
+    def set_builder(self, type: str = "CURRENT") -> PluginArgsBuilder:
+        if type == "CURRENT":
+            self._builder = CurrentPluginArgsBuilder()
+        return self._builder
+
+class CurrentPluginArgsBuilder(PluginArgsBuilder):
+    def __init__(self, species: str = None, assembly: str = None, version: int = None) -> None:
+        self.matcher = RepoPluginConfigMatcher()
+        self.species = species
+        self._assembly = assembly
+        self._version = version
+
+        # REMOVE THIS!! /nfs/production/flicek/ensembl/variation/enseweb-data_tools
+        self.base_path = f"{os.environ['PLUGIN_DATA_DIR']}/grch38/e{str(version)}/vep/plugin_data"
+        if self._assembly == "GRCh37":
+            self.base_path = self.base_path.replace("grch38", "grch37")
+
+    @property
+    def assembly(self):
+        return self._assembly
+    
+    @assembly.setter
+    def assembly(self, assembly):
+        self._assembly = assembly
+        if self._assembly == "GRCh37":
+            self.base_path = self.base_path.replace("grch38", "grch37")
+
+        return self._assembly
+    
+    @property
+    def version(self):
+        return self._version
+    
+    @version.setter
+    def version(self, version: int):
+        self.base_path = self.base_path.replace(str(self._version), str(version))
+        self._version = version
+
+        return self._version
+
+    def match(self, plugin_name: str) -> bool:
+        return self.matcher.match(plugin_name, self.species)
+    
+    def get_args(self, plugin_name: str) -> Dict:
+        if plugin_name == "CADD":
+            # CADD have data v1.7 data file from e113
+            if self._version < 113:
+                self.base_path = self.base_path.replace(f"{self._version}", "113")
+
+            if self.species == "sus_scrofa":
+                snv = os.path.join(self.base_path, "ALL_pCADD-PHRED-scores.tsv.gz")
+                self.check_plugin_files(plugin_name, [snv])
+
+                return {"snv": snv}
+
+            snv = os.path.join(
+                self.base_path, f"CADD_{self._assembly}_1.7_whole_genome_SNVs.tsv.gz"
+            )
+            indels = os.path.join(self.base_path, f"CADD_{self._assembly}_1.7_InDels.tsv.gz")
+
+            self.check_plugin_files(plugin_name, [snv, indels])
+
+            return {"snv": snv, "indels": indels}
+
+        if plugin_name == "REVEL":
+            data_file = f"/nfs/production/flicek/ensembl/variation/data/REVEL/2021-may/new_tabbed_revel_{self._assembly.lower()}.tsv.gz"
+
+            self.check_plugin_files(plugin_name, [data_file])
+
+            return {"data_file": data_file}
+
+        if plugin_name == "SpliceAI":
+            ucsc_assembly = "hg38" if self._assembly == "GRCh38" else "hg19"
+            snv = os.path.join(
+                self.base_path, f"spliceai_scores.masked.snv.{ucsc_assembly}.vcf.gz"
+            )
+            indels = os.path.join(
+                self.base_path, f"spliceai_scores.masked.indel.{ucsc_assembly}.vcf.gz"
+            )
+
+            self.check_plugin_files(plugin_name, [snv, indels])
+
+            return {"snv": snv, "indel": indels}
+
+        if plugin_name == "Phenotypes":
+            pl_assembly = f"_{self._assembly}" if self.species == "homo_sapiens" else ""
+            file = os.path.join(
+                self.base_path,
+                f"Phenotypes_data_files/Phenotypes.pm_{self.species}_{self._version}{pl_assembly}.gvf.gz",
+            )
+
+            if not self.check_plugin_files(plugin_name, [file], "skip"):
+                return None
+
+            return {
+                "file": file, 
+                "id_match": 1, 
+                "cols": "phenotype&source&id&type&clinvar_clin_sig"
+            }
+
+        if plugin_name == "IntAct":
+            mutation_file = os.path.join(self.base_path, "mutations.tsv")
+            mapping_file = os.path.join(self.base_path, "mutation_gc_map.txt.gz")
+
+            self.check_plugin_files(plugin_name, [mutation_file, mapping_file])
+
+            return {
+                "mutation_file": mutation_file,
+                "mapping_file": mapping_file,
+                "pmid": 1
+            }
+
+        if plugin_name == "AncestralAllele":
+            # TMP - 110 datafile has 109 in the file name
+            pl_version = "109" if self._assembly == "GRCh38" else "e75"
+            file = os.path.join(
+                self.base_path, f"homo_sapiens_ancestor_{self._assembly}_{pl_version}.fa.gz"
+            )
+
+            self.check_plugin_files(plugin_name, [file])
+
+            return {"file": file}
+
+        if plugin_name == "Conservation":
+            conservation_data_dir = "/nfs/production/flicek/ensembl/variation/data/Conservation"
+            file = os.path.join(
+                conservation_data_dir, f"gerp_conservation_scores.{self.species}.{self._assembly}.bw"
+            )
+
+            if not self.check_plugin_files(plugin_name, [file], "skip"):
+                return None
+
+            return {"file": file}
+
+        if plugin_name == "MaveDB":
+            file = os.path.join(self.base_path, "MaveDB_variants.tsv.gz")
+
+            if not self.check_plugin_files(plugin_name, [file], "skip"):
+                return None
+
+            return {
+                "file": file,
+                "cols": "MaveDB_score:MaveDB_urn",
+                "transcript_match": 1
+            }
+
+        if plugin_name == "AlphaMissense":
+            # Alphamissense do not have data file in e110 directory or below
+            if self._version < 111:
+                self.base_path = self.base_path.replace(f"{self._version}", "111")
+            file = os.path.join(self.base_path, "AlphaMissense_hg38.tsv.gz")
+
+            if not self.check_plugin_files(plugin_name, [file], "skip"):
+                return None
+
+            return {"file": file}
+
+        if plugin_name == "ClinPred":
+            # ClinPred do not have data file in e113 directory or below
+            if self._version < 113:
+                self.base_path = self.base_path.replace(f"{self._version}", "113")
+            file_name = (
+                "ClinPred_hg38_sorted_tabbed.tsv.gz"
+                if self._assembly == "GRCh38"
+                else "ClinPred_tabbed.tsv.gz"
+            )
+            file = os.path.join(self.base_path, "ClinPred", file_name)
+
+            if not self.check_plugin_files(plugin_name, [file], "skip"):
+                return None
+
+            return {"file": file}
+
+        return None
+
+
+    def check_plugin_files(self, plugin: str, files: List, exit_rule: str = "exit") -> bool:
+        """Verify presence of plugin data files.
+
+        Args:
+            plugin (str): Plugin name for logging.
+            files (list): List of file paths to check.
+            exit_rule (str): 'exit' to raise on missing file, 'skip' to return False.
+
+        Returns:
+            bool: True if all files exist, False if skipped due to exit_rule 'skip'.
+
+        Raises:
+            FileNotFoundError: If a required file is missing and exit_rule is 'exit'.
+        """
+        for file in files:
+            if not os.path.isfile(file):
+                if exit_rule == "skip":
+                    print(f"[INFO] Cannot get {plugin} data file - {file}. Skipping ...")
+                    return False
+
+                raise FileNotFoundError(
+                    f"[ERROR] Cannot get {plugin} data file - {file}. Exiting ..."
+                )
+
+        return True
+
+class RepoPluginConfigMatcher():
+    REPO_DIR = os.environ["ENSEMBL_ROOT_DIR"]
+    def __init__(
+                self,
+                repo_dir: str = REPO_DIR,
+                config_filename: str = "plugin_config.txt"
+            ):
+
+        self.repo_dir = repo_dir
+        self.config_file = os.path.join(
+                self.repo_dir,
+                "VEP_plugins",
+                config_filename
+            )
+
+    def match(self, plugin_name: str, species) -> bool:
+
+        cmd_generate_plugin_config_json = "use JSON;"
+        cmd_generate_plugin_config_json += f"open IN, '{self.config_file}';"
+        cmd_generate_plugin_config_json += "my @content = <IN>;"
+        cmd_generate_plugin_config_json += "close IN;"
+        cmd_generate_plugin_config_json += (
+            "my $VEP_PLUGIN_CONFIG = eval join('', @content);"
+        )
+        cmd_generate_plugin_config_json += "print encode_json($VEP_PLUGIN_CONFIG);"
+
+        process = subprocess.run(
+            ["perl", "-e", cmd_generate_plugin_config_json],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+        )
+        if process.returncode != 0:
+            print(
+                f"[ERROR] Cannot read plugin config file - {self.config_file}"
+                + "\tError{process.stderr.decode()}\nExiting ..."
+            )
+            return False
+
+        plugin_config = json.loads(process.stdout)
+
+        if "plugins" in plugin_config:
+            for plugin in plugin_config["plugins"]:
+                if plugin["key"] == plugin_name:
+                    if "species" not in plugin:
+                        return True
+                    else:
+                        return species in plugin["species"]
+        else:
+            print(f"[WARNING] No plugin could be found in config {self.config_file}")
+        
+        print(f"[WARNING] Could not find {plugin_name} in config {self.config_file}")
+        return False
\ No newline at end of file
diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml
new file mode 100644
index 00000000..f23200a2
--- /dev/null
+++ b/src/python/pyproject.toml
@@ -0,0 +1,64 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+[project]
+name = "ensembl-variation-utils"
+description = "Ensembl Variation Pipeline"
+requires-python = ">= 3.9"
+version = "0.0.1"
+readme = "README.md"
+authors = [
+    {name = "Syed Nakib Hossain", email = "snhossain@ebi.ac.uk"},
+]
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE"]
+keywords = [
+    "ensembl",
+    "bioinformatics",
+    "pipeline",
+    "variation",
+]
+classifiers = [
+    "Private :: Do Not Upload",
+    "Development Status :: 2 - Pre-Alpha",
+    "Environment :: Console",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+	"Deprecated >= 1.2.18",
+    "mkdocs >= 1.6.1"
+]
+
+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+ignore-vcs = true
+include = [
+  "ensembl/variation_utils/**"
+]
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.lint]
+ignore = []
+
+[tool.ruff.format]
+quote-style = "double"
+docstring-code-format = true
\ No newline at end of file
diff --git a/src/python/test.vcf b/src/python/test.vcf
new file mode 100644
index 00000000..a5455e4f
--- /dev/null
+++ b/src/python/test.vcf
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.2
+#CHROM	POS ID	REF	ALT
+1	2	.	A	G
diff --git a/src/python/tests/backup.py b/src/python/tests/backup.py
new file mode 100644
index 00000000..7e8c36d8
--- /dev/null
+++ b/src/python/tests/backup.py
@@ -0,0 +1,1524 @@
+import pytest
+import tempfile
+import os
+from unittest.mock import Mock, MagicMock
+from typing import Dict, Any
+import configparser
+
+# Import the classes from your main module
+# from file_locator_api import *  # Assuming the API is in file_locator_api.py
+from file_locator_api import (
+    MetadataDBClient, MetadataGRPCClient, FTPGFFLocator, FTPFASTALocator,
+    VEPCacheLocator, FileLocatorAPI, InfrastructureType, DatasetType,
+    MetadataDBClientFactory, FileLocatorFactory
+)
+
+
+@pytest.fixture
+def mock_metadata_client():
+    """Mock metadata client for testing"""
+    client = Mock()
+    client.get_assembly_accession.return_value = "GCA_000001405.29"
+    client.get_scientific_name.return_value = "homo_sapiens"
+    client.get_dataset_uuid.return_value = "dataset-uuid-123"
+    client.get_dataset_attribute_value.return_value = "test_value"
+    client.configure.return_value = None
+    return client
+
+
+@pytest.fixture
+def sample_genome_uuid():
+    """Sample genome UUID for testing"""
+    return "genome-uuid-12345"
+
+
+@pytest.fixture
+def temp_directory():
+    """Temporary directory for file operations"""
+    with tempfile.TemporaryDirectory() as temp_dir:
+        yield temp_dir
+
+
+@pytest.fixture
+def mock_ini_file(temp_directory):
+    """Create a mock INI configuration file"""
+    config = configparser.ConfigParser()
+    config['database'] = {
+        'host': 'localhost',
+        'port': '3306',
+        'user': 'testuser',
+        'password': 'testpass',
+        'dbname': 'testdb'
+    }
+    
+    ini_path = os.path.join(temp_directory, 'test_config.ini')
+    with open(ini_path, 'w') as f:
+        config.write(f)
+    
+    return ini_path
+
+
+@pytest.fixture
+def db_client_config():
+    """Database client configuration"""
+    return {
+        'host': 'test-host',
+        'port': 3306,
+        'user': 'test-user',
+        'password': 'test-pass',
+        'dbname': 'test-db'
+    }
+
+
+@pytest.fixture
+def sample_file_paths():
+    """Sample file paths for testing"""
+    return {
+        'gff': 'homo_sapiens/GCA_000001405.29/ensembl.gff3',
+        'fasta': 'homo_sapiens/GCA_000001405.29.fa',
+        'vep_cache': 'vep_cache/homo_sapiens_GCA_000001405.29'
+    }
+
+
+# tests/test_metadata_clients.py
+"""Tests for metadata client classes"""
+
+import pytest
+from unittest.mock import Mock, patch, MagicMock
+from file_locator_api import (
+    MetadataDBClient, MetadataGRPCClient, MetadataDBClientFactory,
+    MetadataGRPCClientFactory
+)
+
+
+class TestMetadataDBClient:
+    """Test cases for MetadataDBClient"""
+    
+    def test_init(self, db_client_config):
+        """Test MetadataDBClient initialization"""
+        client = MetadataDBClient(
+            host=db_client_config['host'],
+            port=db_client_config['port'],
+            user=db_client_config['user'],
+            password=db_client_config['password'],
+            dbname=db_client_config['dbname']
+        )
+        
+        assert client.host == db_client_config['host']
+        assert client.port == db_client_config['port']
+        assert client.user == db_client_config['user']
+        assert client._password == db_client_config['password']
+        assert client.dbname == db_client_config['dbname']
+    
+    def test_configure(self, db_client_config):
+        """Test configure method"""
+        client = MetadataDBClient(
+            host=db_client_config['host'],
+            port=db_client_config['port'],
+            user=db_client_config['user'],
+            password=db_client_config['password'],
+            dbname=db_client_config['dbname']
+        )
+        
+        # Should not raise an exception
+        client.configure()
+    
+    @patch('file_locator_api.MetadataDBClient._run_query')
+    def test_get_assembly_accession(self, mock_query, db_client_config, sample_genome_uuid):
+        """Test get_assembly_accession method"""
+        client = MetadataDBClient(**db_client_config)
+        mock_query.return_value = "GCA_000001405.29"
+        
+        # This would need actual implementation in the real class
+        # For now, we test that the method exists
+        assert hasattr(client, 'get_assembly_accession')
+    
+    @patch('file_locator_api.MetadataDBClient._run_query')
+    def test_get_scientific_name(self, mock_query, db_client_config, sample_genome_uuid):
+        """Test get_scientific_name method"""
+        client = MetadataDBClient(**db_client_config)
+        mock_query.return_value = "homo_sapiens"
+        
+        assert hasattr(client, 'get_scientific_name')
+
+
+class TestMetadataGRPCClient:
+    """Test cases for MetadataGRPCClient"""
+    
+    def test_init(self):
+        """Test MetadataGRPCClient initialization"""
+        client = MetadataGRPCClient()
+        assert client is not None
+    
+    def test_configure(self):
+        """Test configure method"""
+        client = MetadataGRPCClient()
+        # Should not raise an exception
+        client.configure()
+    
+    def test_methods_exist(self):
+        """Test that all required methods exist"""
+        client = MetadataGRPCClient()
+        assert hasattr(client, 'get_assembly_accession')
+        assert hasattr(client, 'get_scientific_name')
+        assert hasattr(client, 'get_dataset_uuid')
+        assert hasattr(client, 'get_dataset_attribute_value')
+
+
+class TestMetadataClientFactories:
+    """Test cases for metadata client factories"""
+    
+    def test_metadata_client_factory(self):
+        """Test MetadataClientFactory"""
+        from file_locator_api import MetadataClientFactory
+        
+        client = MetadataClientFactory.create()
+        assert isinstance(client, MetadataGRPCClient)
+    
+    def test_metadata_db_client_factory(self, mock_ini_file):
+        """Test MetadataDBClientFactory"""
+        factory = MetadataDBClientFactory(mock_ini_file)
+        client = factory.create()
+        
+        assert isinstance(client, MetadataDBClient)
+        assert client.host == 'localhost'
+        assert client.port == 3306
+        assert client.user == 'testuser'
+    
+    def test_metadata_grpc_client_factory(self):
+        """Test MetadataGRPCClientFactory"""
+        from file_locator_api import MetadataGRPCClientFactory
+        
+        client = MetadataGRPCClientFactory.create()
+        assert isinstance(client, MetadataGRPCClient)
+
+
+# tests/test_file_locators.py
+"""Tests for file locator classes"""
+
+import pytest
+from unittest.mock import Mock, patch, mock_open
+from file_locator_api import (
+    FTPGFFLocator, FTPFASTALocator, OldFTPGFFLocator, OldFTPFASTALocator,
+    VEPCacheLocator, FTPDiskFileLocator, FTPServerFileLocator,
+    GFFLocator, FASTALocator, InfrastructureType
+)
+
+
+class TestFTPGFFLocator:
+    """Test cases for FTPGFFLocator"""
+    
+    def test_init(self, mock_metadata_client):
+        """Test FTPGFFLocator initialization"""
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        assert locator.metadata_client == mock_metadata_client
+        assert locator.scientific_name == ""
+        assert locator.assembly_accession == ""
+        assert locator.annotation_source == ""
+    
+    def test_locate_file(self, mock_metadata_client, sample_genome_uuid):
+        """Test locate_file method"""
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        file_path = locator.locate_file(sample_genome_uuid, "ensembl")
+        
+        assert file_path == "homo_sapiens/GCA_000001405.29/ensembl.gff3"
+        assert locator.scientific_name == "homo_sapiens"
+        assert locator.assembly_accession == "GCA_000001405.29"
+        assert locator.annotation_source == "ensembl"
+    
+    def test_copy_file(self, mock_metadata_client, temp_directory):
+        """Test copy_file method"""
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        result = locator.copy_file(temp_directory)
+        assert result is True
+
+
+class TestFTPFASTALocator:
+    """Test cases for FTPFASTALocator"""
+    
+    def test_init(self, mock_metadata_client):
+        """Test FTPFASTALocator initialization"""
+        locator = FTPFASTALocator(mock_metadata_client)
+        
+        assert locator.metadata_client == mock_metadata_client
+        assert locator.production_name == ""
+        assert locator.assembly_accession == ""
+    
+    def test_locate_file(self, mock_metadata_client, sample_genome_uuid):
+        """Test locate_file method"""
+        locator = FTPFASTALocator(mock_metadata_client)
+        
+        file_path = locator.locate_file(sample_genome_uuid)
+        
+        assert file_path == "homo_sapiens/GCA_000001405.29.fa"
+        assert locator.production_name == "homo_sapiens"
+        assert locator.assembly_accession == "GCA_000001405.29"
+    
+    def test_copy_file(self, mock_metadata_client, temp_directory):
+        """Test copy_file method"""
+        locator = FTPFASTALocator(mock_metadata_client)
+        
+        result = locator.copy_file(temp_directory)
+        assert result is True
+
+
+class TestVEPCacheLocator:
+    """Test cases for VEPCacheLocator"""
+    
+    def test_init(self, mock_metadata_client):
+        """Test VEPCacheLocator initialization"""
+        locator = VEPCacheLocator(mock_metadata_client)
+        
+        assert locator.metadata_client == mock_metadata_client
+        assert locator.production_name == ""
+        assert locator.assembly_accession == ""
+    
+    def test_get_path(self, mock_metadata_client, sample_genome_uuid):
+        """Test get_path method"""
+        locator = VEPCacheLocator(mock_metadata_client)
+        
+        cache_path = locator.get_path(sample_genome_uuid)
+        
+        assert cache_path == "vep_cache/homo_sapiens_GCA_000001405.29"
+        assert locator.production_name == "homo_sapiens"
+        assert locator.assembly_accession == "GCA_000001405.29"
+    
+    def test_copy_to(self, mock_metadata_client, temp_directory):
+        """Test copy_to method"""
+        locator = VEPCacheLocator(mock_metadata_client)
+        
+        result = locator.copy_to(temp_directory)
+        assert result is True
+
+
+class TestFTPFileLocators:
+    """Test cases for FTP file locators"""
+    
+    def test_ftp_disk_file_locator(self):
+        """Test FTPDiskFileLocator"""
+        base_path = "/data/ftp"
+        locator = FTPDiskFileLocator(base_path)
+        
+        assert locator.base_path == base_path
+        
+        file_path = locator.locate_file("test/file.txt")
+        assert file_path == "/data/ftp/test/file.txt"
+    
+    def test_ftp_server_file_locator(self):
+        """Test FTPServerFileLocator"""
+        base_path = "pub/data"
+        server = "ftp.example.com"
+        locator = FTPServerFileLocator(base_path, server)
+        
+        assert locator.base_path == base_path
+        assert locator.server == server
+        
+        file_path = locator.locate_file("test/file.txt")
+        assert file_path == "ftp://ftp.example.com/pub/data/test/file.txt"
+
+
+class TestGenericFileLocators:
+    """Test cases for generic file locators"""
+    
+    def test_gff_locator_set_locator(self):
+        """Test GFFLocator set_locator method"""
+        locator = GFFLocator()
+        
+        disk_locator = locator.set_locator(InfrastructureType.DISK)
+        assert isinstance(disk_locator, FTPDiskFileLocator)
+        
+        server_locator = locator.set_locator(InfrastructureType.SERVER)
+        assert isinstance(server_locator, FTPServerFileLocator)
+    
+    def test_fasta_locator_set_locator(self):
+        """Test FASTALocator set_locator method"""
+        locator = FASTALocator()
+        
+        disk_locator = locator.set_locator(InfrastructureType.DISK)
+        assert isinstance(disk_locator, FTPDiskFileLocator)
+        
+        server_locator = locator.set_locator(InfrastructureType.SERVER)
+        assert isinstance(server_locator, FTPServerFileLocator)
+    
+    def test_gff_locator_without_set_locator(self):
+        """Test GFFLocator methods without setting locator"""
+        locator = GFFLocator()
+        
+        with pytest.raises(ValueError, match="Locator not set"):
+            locator.locate_file("test")
+        
+        result = locator.copy_file("/tmp")
+        assert result is False
+
+
+# tests/test_factories.py
+"""Tests for factory classes"""
+
+import pytest
+from file_locator_api import (
+    FileLocatorFactory, DatasetType, InfrastructureType,
+    FTPGFFLocator, FTPFASTALocator, OldFTPGFFLocator, OldFTPFASTALocator,
+    VEPCacheLocator
+)
+
+
+class TestFileLocatorFactory:
+    """Test cases for FileLocatorFactory"""
+    
+    def test_create_gff_locator_server(self, mock_metadata_client):
+        """Test creating GFF locator for server infrastructure"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.GFF, InfrastructureType.SERVER, mock_metadata_client
+        )
+        assert isinstance(locator, FTPGFFLocator)
+    
+    def test_create_gff_locator_disk(self, mock_metadata_client):
+        """Test creating GFF locator for disk infrastructure"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.GFF, InfrastructureType.DISK, mock_metadata_client
+        )
+        assert isinstance(locator, OldFTPGFFLocator)
+    
+    def test_create_fasta_locator_server(self, mock_metadata_client):
+        """Test creating FASTA locator for server infrastructure"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.FASTA, InfrastructureType.SERVER, mock_metadata_client
+        )
+        assert isinstance(locator, FTPFASTALocator)
+    
+    def test_create_fasta_locator_disk(self, mock_metadata_client):
+        """Test creating FASTA locator for disk infrastructure"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.FASTA, InfrastructureType.DISK, mock_metadata_client
+        )
+        assert isinstance(locator, OldFTPFASTALocator)
+    
+    def test_create_vep_cache_locator(self, mock_metadata_client):
+        """Test creating VEP cache locator"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.VEP_CACHE, InfrastructureType.SERVER, mock_metadata_client
+        )
+        assert isinstance(locator, VEPCacheLocator)
+    
+    def test_unsupported_dataset_type(self, mock_metadata_client):
+        """Test creating locator with unsupported dataset type"""
+        with pytest.raises(ValueError, match="Unsupported dataset type"):
+            # Create a mock dataset type that doesn't exist
+            fake_type = Mock()
+            fake_type.value = "unsupported"
+            FileLocatorFactory.create_locator(
+                fake_type, InfrastructureType.SERVER, mock_metadata_client
+            )
+
+
+# tests/test_api.py
+"""Tests for main FileLocatorAPI class"""
+
+import pytest
+from unittest.mock import Mock, patch, MagicMock
+from file_locator_api import (
+    FileLocatorAPI, InfrastructureType, DatasetType
+)
+
+
+class TestFileLocatorAPI:
+    """Test cases for FileLocatorAPI"""
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    def test_init(self, mock_factory_class):
+        """Test FileLocatorAPI initialization"""
+        mock_factory = Mock()
+        mock_client = Mock()
+        mock_factory.create.return_value = mock_client
+        mock_factory_class.return_value = mock_factory
+        
+        api = FileLocatorAPI("test_config.ini")
+        
+        assert api.metadata_client == mock_client
+        mock_factory_class.assert_called_once_with("test_config.ini")
+        mock_factory.create.assert_called_once()
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    @patch('file_locator_api.FileLocatorFactory')
+    def test_locate_gff_file(self, mock_locator_factory, mock_client_factory, sample_genome_uuid):
+        """Test locate_gff_file method"""
+        # Setup mocks
+        mock_client = Mock()
+        mock_client_factory.return_value.create.return_value = mock_client
+        
+        mock_locator = Mock()
+        mock_locator.locate_file.return_value = "test/path.gff3"
+        mock_locator_factory.create_locator.return_value = mock_locator
+        
+        api = FileLocatorAPI()
+        result = api.locate_gff_file(sample_genome_uuid, "ensembl")
+        
+        assert result == "test/path.gff3"
+        mock_locator_factory.create_locator.assert_called_once_with(
+            DatasetType.GFF, InfrastructureType.SERVER, mock_client
+        )
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    @patch('file_locator_api.FileLocatorFactory')
+    def test_locate_fasta_file(self, mock_locator_factory, mock_client_factory, sample_genome_uuid):
+        """Test locate_fasta_file method"""
+        # Setup mocks
+        mock_client = Mock()
+        mock_client_factory.return_value.create.return_value = mock_client
+        
+        mock_locator = Mock()
+        mock_locator.locate_file.return_value = "test/path.fa"
+        mock_locator_factory.create_locator.return_value = mock_locator
+        
+        api = FileLocatorAPI()
+        result = api.locate_fasta_file(sample_genome_uuid)
+        
+        assert result == "test/path.fa"
+        mock_locator_factory.create_locator.assert_called_once_with(
+            DatasetType.FASTA, InfrastructureType.SERVER, mock_client
+        )
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    @patch('file_locator_api.VEPCacheLocator')
+    def test_get_vep_cache_path(self, mock_vep_class, mock_client_factory, sample_genome_uuid):
+        """Test get_vep_cache_path method"""
+        # Setup mocks
+        mock_client = Mock()
+        mock_client_factory.return_value.create.return_value = mock_client
+        
+        mock_vep_locator = Mock()
+        mock_vep_locator.get_path.return_value = "vep_cache/test_path"
+        mock_vep_class.return_value = mock_vep_locator
+        
+        api = FileLocatorAPI()
+        result = api.get_vep_cache_path(sample_genome_uuid)
+        
+        assert result == "vep_cache/test_path"
+        mock_vep_class.assert_called_once_with(mock_client)
+        mock_vep_locator.get_path.assert_called_once_with(sample_genome_uuid)
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    @patch('file_locator_api.FileLocatorFactory')
+    def test_copy_files(self, mock_locator_factory, mock_client_factory, sample_genome_uuid, temp_directory):
+        """Test copy_files method"""
+        # Setup mocks
+        mock_client = Mock()
+        mock_client_factory.return_value.create.return_value = mock_client
+        
+        mock_locator = Mock()
+        mock_locator.copy_file.return_value = True
+        mock_locator_factory.create_locator.return_value = mock_locator
+        
+        api = FileLocatorAPI()
+        file_types = [DatasetType.GFF, DatasetType.FASTA]
+        results = api.copy_files(sample_genome_uuid, temp_directory, file_types)
+        
+        assert results == {'gff': True, 'fasta': True}
+        assert mock_locator_factory.create_locator.call_count == 2
+        assert mock_locator.copy_file.call_count == 2
+    
+    @patch('file_locator_api.MetadataDBClientFactory')
+    @patch('file_locator_api.FileLocatorFactory')
+    def test_copy_files_with_exception(self, mock_locator_factory, mock_client_factory, sample_genome_uuid, temp_directory):
+        """Test copy_files method with exception handling"""
+        # Setup mocks
+        mock_client = Mock()
+        mock_client_factory.return_value.create.return_value = mock_client
+        
+        mock_locator_factory.create_locator.side_effect = Exception("Test error")
+        
+        api = FileLocatorAPI()
+        file_types = [DatasetType.GFF]
+        results = api.copy_files(sample_genome_uuid, temp_directory, file_types)
+        
+        assert results == {'gff': False}
+
+
+# tests/test_integration.py
+"""Integration tests for the entire file locator system"""
+
+import pytest
+import tempfile
+import os
+from unittest.mock import Mock, patch
+from file_locator_api import (
+    FileLocatorAPI, DatasetType, InfrastructureType,
+    MetadataDBClient, FTPGFFLocator, FTPFASTALocator
+)
+
+
+class TestIntegration:
+    """Integration test cases"""
+    
+    @pytest.fixture
+    def mock_database_connection(self):
+        """Mock database connection for integration tests"""
+        with patch('file_locator_api.MetadataDBClient._run_query') as mock_query:
+            yield mock_query
+    
+    def test_full_workflow_gff_location(self, mock_ini_file, sample_genome_uuid):
+        """Test complete workflow for locating GFF files"""
+        with patch('file_locator_api.MetadataDBClient.get_scientific_name') as mock_name, \
+             patch('file_locator_api.MetadataDBClient.get_assembly_accession') as mock_acc:
+            
+            mock_name.return_value = "homo_sapiens"
+            mock_acc.return_value = "GCA_000001405.29"
+            
+            api = FileLocatorAPI(mock_ini_file)
+            result = api.locate_gff_file(sample_genome_uuid, "ensembl")
+            
+            assert "homo_sapiens" in result
+            assert "GCA_000001405.29" in result
+            assert "ensembl.gff3" in result
+    
+    def test_full_workflow_multiple_files(self, mock_ini_file, sample_genome_uuid):
+        """Test complete workflow for handling multiple file types"""
+        with patch('file_locator_api.MetadataDBClient.get_scientific_name') as mock_name, \
+             patch('file_locator_api.MetadataDBClient.get_assembly_accession') as mock_acc, \
+             patch('file_locator_api.FileLocator.copy_file') as mock_copy:
+            
+            mock_name.return_value = "homo_sapiens"
+            mock_acc.return_value = "GCA_000001405.29"
+            mock_copy.return_value = True
+            
+            api = FileLocatorAPI(mock_ini_file)
+            
+            with tempfile.TemporaryDirectory() as temp_dir:
+                results = api.copy_files(
+                    sample_genome_uuid, 
+                    temp_dir, 
+                    [DatasetType.GFF, DatasetType.FASTA, DatasetType.VEP_CACHE]
+                )
+                
+                assert len(results) == 3
+                assert all(results.values())
+    
+    def test_error_handling_integration(self, mock_ini_file, sample_genome_uuid):
+        """Test error handling in integration scenario"""
+        with patch('file_locator_api.MetadataDBClient.get_scientific_name') as mock_name:
+            mock_name.side_effect = Exception("Database connection failed")
+            
+            api = FileLocatorAPI(mock_ini_file)
+            
+            # Should handle exceptions gracefully
+            with tempfile.TemporaryDirectory() as temp_dir:
+                results = api.copy_files(sample_genome_uuid, temp_dir, [DatasetType.GFF])
+                assert results['gff'] is False
+
+
+# tests/test_performance.py
+"""Performance tests for the file locator system"""
+
+import pytest
+import time
+from unittest.mock import Mock, patch
+from file_locator_api import FileLocatorAPI, DatasetType
+
+
+class TestPerformance:
+    """Performance test cases"""
+    
+    @pytest.mark.performance
+    def test_multiple_file_location_performance(self, mock_ini_file):
+        """Test performance of locating multiple files"""
+        with patch('file_locator_api.MetadataDBClient.get_scientific_name') as mock_name, \
+             patch('file_locator_api.MetadataDBClient.get_assembly_accession') as mock_acc:
+            
+            mock_name.return_value = "homo_sapiens"
+            mock_acc.return_value = "GCA_000001405.29"
+            
+            api = FileLocatorAPI(mock_ini_file)
+            
+            start_time = time.time()
+            
+            # Locate 100 files
+            for i in range(100):
+                genome_uuid = f"genome-{i}"
+                api.locate_gff_file(genome_uuid, "ensembl")
+                api.locate_fasta_file(genome_uuid)
+                api.get_vep_cache_path(genome_uuid)
+            
+            end_time = time.time()
+            duration = end_time - start_time
+            
+            # Should complete within reasonable time (adjust threshold as needed)
+            assert duration < 5.0, f"Performance test took {duration:.2f} seconds"
+    
+    @pytest.mark.performance
+    def test_concurrent_file_operations(self, mock_ini_file):
+        """Test concurrent file operations"""
+        import threading
+        
+        with patch('file_locator_api.MetadataDBClient.get_scientific_name') as mock_name, \
+             patch('file_locator_api.MetadataDBClient.get_assembly_accession') as mock_acc:
+            
+            mock_name.return_value = "homo_sapiens"
+            mock_acc.return_value = "GCA_000001405.29"
+            
+            api = FileLocatorAPI(mock_ini_file)
+            results = []
+            
+            def locate_files(genome_id):
+                result = api.locate_gff_file(f"genome-{genome_id}", "ensembl")
+                results.append(result)
+            
+            # Run 10 concurrent operations
+            threads = []
+            for i in range(10):
+                thread = threading.Thread(target=locate_files, args=(i,))
+                threads.append(thread)
+                thread.start()
+            
+            # Wait for all threads to complete
+            for thread in threads:
+                thread.join()
+            
+            assert len(results) == 10
+            assert all("homo_sapiens" in result for result in results)
+
+
+# tests/pytest.ini
+"""
+[tool:pytest]
+testpaths = tests
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+addopts = 
+    -v
+    --strict-markers
+    --strict-config
+    --tb=short
+markers =
+    performance: marks tests as performance tests (deselect with '-m "not performance"')
+    integration: marks tests as integration tests
+    unit: marks tests as unit tests
+filterwarnings =
+    ignore::DeprecationWarning
+"""
+
+
+# tests/test_edge_cases.py
+"""Tests for edge cases and error conditions"""
+
+import pytest
+from unittest.mock import Mock
+from file_locator_api import (
+    FileLocatorAPI, DatasetType, InfrastructureType,
+    FileLocatorFactory, VEPCacheLocator
+)
+
+
+class TestEdgeCases:
+    """Test edge cases and error conditions"""
+    
+    def test_empty_genome_uuid(self, mock_metadata_client):
+        """Test behavior with empty genome UUID"""
+        locator = VEPCacheLocator(mock_metadata_client)
+        
+        # Should handle empty UUID gracefully
+        result = locator.get_path("")
+        assert isinstance(result, str)
+    
+    def test_none_metadata_values(self, sample_genome_uuid):
+        """Test behavior when metadata returns None"""
+        mock_client = Mock()
+        mock_client.get_scientific_name.return_value = None
+        mock_client.get_assembly_accession.return_value = None
+        
+        locator = VEPCacheLocator(mock_client)
+        result = locator.get_path(sample_genome_uuid)
+        
+        # Should handle None values without crashing
+        assert isinstance(result, str)
+    
+    def test_invalid_file_paths(self, mock_metadata_client):
+        """Test behavior with invalid file paths"""
+        mock_metadata_client.get_scientific_name.return_value = "invalid/path/with/slashes"
+        mock_metadata_client.get_assembly_accession.return_value = "invalid\\path\\with\\backslashes"
+        
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        # Should handle invalid characters in paths
+        result = locator.locate_file("test-genome", "ensembl")
+        assert isinstance(result, str)
+        assert "ensembl.gff3" in result
+    
+    def test_missing_annotation_source(self, mock_metadata_client, sample_genome_uuid):
+        """Test behavior with missing annotation source"""
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        # Test with empty annotation source
+        result = locator.locate_file(sample_genome_uuid, "")
+        assert isinstance(result, str)
+        assert ".gff3" in result
+    
+    def test_large_genome_uuid(self, mock_metadata_client):
+        """Test behavior with very large genome UUID"""
+        large_uuid = "x" * 1000  # 1000 character UUID
+        
+        from file_locator_api import VEPCacheLocator
+        locator = VEPCacheLocator(mock_metadata_client)
+        
+        # Should handle large UUIDs without issues
+        result = locator.get_path(large_uuid)
+        assert isinstance(result, str)
+
+
+# tests/test_mocking.py
+"""Advanced mocking tests for complex scenarios"""
+
+import pytest
+from unittest.mock import Mock, patch, MagicMock, call
+from file_locator_api import (
+    FileLocatorAPI, MetadataDBClient, FTPGFFLocator,
+    DatasetType, InfrastructureType
+)
+
+
+class TestAdvancedMocking:
+    """Advanced mocking test cases"""
+    
+    @patch.multiple(
+        'file_locator_api.MetadataDBClient',
+        get_scientific_name=Mock(return_value="test_species"),
+        get_assembly_accession=Mock(return_value="test_assembly"),
+        configure=Mock()
+    )
+    def test_patch_multiple_metadata_methods(self, sample_genome_uuid):
+        """Test patching multiple methods at once"""
+        from file_locator_api import MetadataDBClient
+        
+        client = MetadataDBClient("host", 3306, "user", "pass", "db")
+        
+        assert client.get_scientific_name(sample_genome_uuid) == "test_species"
+        assert client.get_assembly_accession(sample_genome_uuid) == "test_assembly"
+    
+    def test_side_effect_sequence(self, mock_metadata_client, sample_genome_uuid):
+        """Test using side_effect with sequence of return values"""
+        mock_metadata_client.get_scientific_name.side_effect = [
+            "species1", "species2", "species3"
+        ]
+        
+        from file_locator_api import FTPFASTALocator
+        locator = FTPFASTALocator(mock_metadata_client)
+        
+        # Each call should return different species
+        result1 = locator.locate_file(f"{sample_genome_uuid}_1")
+        result2 = locator.locate_file(f"{sample_genome_uuid}_2")
+        result3 = locator.locate_file(f"{sample_genome_uuid}_3")
+        
+        assert "species1" in result1
+        assert "species2" in result2
+        assert "species3" in result3
+    
+    def test_mock_call_assertions(self, mock_metadata_client, sample_genome_uuid):
+        """Test detailed call assertions"""
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        locator.locate_file(sample_genome_uuid, "ensembl")
+        
+        # Verify exact calls were made
+        mock_metadata_client.get_scientific_name.assert_called_once_with(sample_genome_uuid)
+        mock_metadata_client.get_assembly_accession.assert_called_once_with(sample_genome_uuid)
+        
+        # Verify call count
+        assert mock_metadata_client.get_scientific_name.call_count == 1
+        assert mock_metadata_client.get_assembly_accession.call_count == 1
+    
+    def test_context_manager_mocking(self, sample_genome_uuid):
+        """Test mocking with context managers"""
+        with patch('file_locator_api.MetadataDBClient') as mock_client_class:
+            mock_instance = Mock()
+            mock_instance.get_scientific_name.return_value = "context_species"
+            mock_instance.get_assembly_accession.return_value = "context_assembly"
+            mock_client_class.return_value = mock_instance
+            
+            from file_locator_api import FTPFASTALocator
+            client = mock_client_class("host", 3306, "user", "pass", "db")
+            locator = FTPFASTALocator(client)
+            
+            result = locator.locate_file(sample_genome_uuid)
+            
+            assert "context_species" in result
+            assert "context_assembly" in result
+
+
+# tests/test_fixtures_advanced.py
+"""Advanced fixture usage and parametrized tests"""
+
+import pytest
+from file_locator_api import (
+    DatasetType, InfrastructureType, FileLocatorFactory
+)
+
+
+class TestParametrized:
+    """Parametrized test cases"""
+    
+    @pytest.mark.parametrize("dataset_type,expected_class_name", [
+        (DatasetType.GFF, "FTPGFFLocator"),
+        (DatasetType.FASTA, "FTPFASTALocator"),
+        (DatasetType.VEP_CACHE, "VEPCacheLocator")
+    ])
+    def test_factory_creates_correct_locator_server(self, dataset_type, expected_class_name, mock_metadata_client):
+        """Test factory creates correct locator types for server infrastructure"""
+        locator = FileLocatorFactory.create_locator(
+            dataset_type, InfrastructureType.SERVER, mock_metadata_client
+        )
+        assert locator.__class__.__name__ == expected_class_name
+    
+    @pytest.mark.parametrize("genome_uuid,annotation_source", [
+        ("genome-001", "ensembl"),
+        ("genome-002", "refseq"),
+        ("genome-003", "gencode"),
+        ("test-uuid-123", "custom")
+    ])
+    def test_gff_locator_various_inputs(self, genome_uuid, annotation_source, mock_metadata_client):
+        """Test GFF locator with various input combinations"""
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        result = locator.locate_file(genome_uuid, annotation_source)
+        
+        assert annotation_source in result
+        assert ".gff3" in result
+    
+    @pytest.mark.parametrize("infra_type", [
+        InfrastructureType.DISK,
+        InfrastructureType.SERVER
+    ])
+    def test_all_infrastructure_types(self, infra_type, mock_metadata_client):
+        """Test all infrastructure types work"""
+        locator = FileLocatorFactory.create_locator(
+            DatasetType.GFF, infra_type, mock_metadata_client
+        )
+        assert locator is not None
+    
+    @pytest.fixture(params=[
+        ("host1", 3306, "user1", "pass1", "db1"),
+        ("host2", 5432, "user2", "pass2", "db2"),
+        ("localhost", 3307, "testuser", "testpass", "testdb")
+    ])
+    def db_configs(self, request):
+        """Parametrized fixture for different database configurations"""
+        return request.param
+    
+    def test_metadata_client_various_configs(self, db_configs):
+        """Test metadata client with various configurations"""
+        from file_locator_api import MetadataDBClient
+        
+        host, port, user, password, dbname = db_configs
+        client = MetadataDBClient(host, port, user, password, dbname)
+        
+        assert client.host == host
+        assert client.port == port
+        assert client.user == user
+        assert client._password == password
+        assert client.dbname == dbname
+
+
+# tests/test_async.py
+"""Tests for potential async operations"""
+
+import pytest
+import asyncio
+from unittest.mock import Mock, AsyncMock, patch
+
+
+class TestAsyncOperations:
+    """Test async-like operations (for future async support)"""
+    
+    @pytest.mark.asyncio
+    async def test_simulated_async_file_copy(self, mock_metadata_client, temp_directory):
+        """Test simulated async file copy operations"""
+        from file_locator_api import FTPGFFLocator
+        
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        async def async_copy_file(target_dir):
+            """Simulate async file copy"""
+            await asyncio.sleep(0.01)  # Simulate I/O delay
+            return locator.copy_file(target_dir)
+        
+        # Test concurrent copies
+        tasks = [
+            async_copy_file(temp_directory) for _ in range(5)
+        ]
+        
+        results = await asyncio.gather(*tasks)
+        assert all(results)
+    
+    @pytest.mark.asyncio
+    async def test_simulated_async_metadata_retrieval(self):
+        """Test simulated async metadata retrieval"""
+        async def async_get_metadata(genome_uuid):
+            """Simulate async metadata retrieval"""
+            await asyncio.sleep(0.01)  # Simulate network delay
+            return {
+                'scientific_name': 'homo_sapiens',
+                'assembly_accession': 'GCA_000001405.29'
+            }
+        
+        # Test concurrent metadata retrieval
+        tasks = [
+            async_get_metadata(f"genome-{i}") for i in range(10)
+        ]
+        
+        results = await asyncio.gather(*tasks)
+        assert len(results) == 10
+        assert all(result['scientific_name'] == 'homo_sapiens' for result in results)
+
+
+# tests/conftest_fixtures.py
+"""Additional fixtures for complex testing scenarios"""
+
+import pytest
+import sqlite3
+import tempfile
+import os
+from unittest.mock import Mock
+
+
+@pytest.fixture(scope="session")
+def temp_database():
+    """Create temporary SQLite database for testing"""
+    with tempfile.NamedTemporaryFile(suffix=".db", delete=False) as tmp_file:
+        db_path = tmp_file.name
+    
+    # Create test database schema
+    conn = sqlite3.connect(db_path)
+    cursor = conn.cursor()
+    
+    cursor.execute("""
+        CREATE TABLE genomes (
+            uuid TEXT PRIMARY KEY,
+            scientific_name TEXT,
+            assembly_accession TEXT
+        )
+    """)
+    
+    cursor.execute("""
+        CREATE TABLE datasets (
+            uuid TEXT PRIMARY KEY,
+            genome_uuid TEXT,
+            dataset_type TEXT,
+            release_id INTEGER
+        )
+    """)
+    
+    # Insert test data
+    test_data = [
+        ("genome-001", "homo_sapiens", "GCA_000001405.29"),
+        ("genome-002", "mus_musculus", "GCA_000001635.9"),
+        ("genome-003", "danio_rerio", "GCA_000002035.4")
+    ]
+    
+    cursor.executemany(
+        "INSERT INTO genomes VALUES (?, ?, ?)", 
+        test_data
+    )
+    
+    conn.commit()
+    conn.close()
+    
+    yield db_path
+    
+    # Cleanup
+    os.unlink(db_path)
+
+
+@pytest.fixture
+def mock_ftp_server():
+    """Mock FTP server for testing file operations"""
+    server_mock = Mock()
+    server_mock.host = "ftp.test.com"
+    server_mock.port = 21
+    server_mock.list_files.return_value = [
+        "homo_sapiens/GCA_000001405.29/ensembl.gff3",
+        "homo_sapiens/GCA_000001405.29.fa",
+        "mus_musculus/GCA_000001635.9/ensembl.gff3",
+        "mus_musculus/GCA_000001635.9.fa"
+    ]
+    return server_mock
+
+
+@pytest.fixture
+def mock_network_delay():
+    """Fixture to simulate network delays"""
+    import time
+    
+    def simulate_delay(seconds=0.1):
+        time.sleep(seconds)
+        return True
+    
+    return simulate_delay
+
+
+@pytest.fixture(scope="class")
+def file_system_setup():
+    """Setup mock file system structure"""
+    with tempfile.TemporaryDirectory() as temp_dir:
+        # Create directory structure
+        species_dirs = ["homo_sapiens", "mus_musculus", "danio_rerio"]
+        
+        for species in species_dirs:
+            species_path = os.path.join(temp_dir, species)
+            os.makedirs(species_path, exist_ok=True)
+            
+            # Create dummy files
+            gff_file = os.path.join(species_path, f"{species}.gff3")
+            fasta_file = os.path.join(species_path, f"{species}.fa")
+            
+            with open(gff_file, 'w') as f:
+                f.write(f"# GFF3 file for {species}\n")
+            
+            with open(fasta_file, 'w') as f:
+                f.write(f">{species}\nACGTACGT\n")
+        
+        yield temp_dir
+
+
+# tests/test_data_validation.py
+"""Tests for data validation and sanitization"""
+
+import pytest
+from file_locator_api import FileLocatorAPI, DatasetType
+
+
+class TestDataValidation:
+    """Test data validation and sanitization"""
+    
+    @pytest.mark.parametrize("invalid_uuid", [
+        None,
+        "",
+        "   ",
+        "genome with spaces",
+        "genome\nwith\nnewlines",
+        "genome\twith\ttabs",
+        "genome;with;semicolons"
+    ])
+    def test_invalid_genome_uuids(self, invalid_uuid, mock_metadata_client):
+        """Test handling of invalid genome UUIDs"""
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        # Should handle invalid UUIDs gracefully
+        try:
+            result = locator.locate_file(invalid_uuid, "ensembl")
+            assert isinstance(result, str)
+        except Exception as e:
+            # If exception is raised, it should be a specific validation error
+            assert "uuid" in str(e).lower() or "invalid" in str(e).lower()
+    
+    @pytest.mark.parametrize("invalid_source", [
+        None,
+        123,  # Non-string
+        [],   # List
+        {},   # Dict
+        "source/with/slashes",
+        "source with spaces"
+    ])
+    def test_invalid_annotation_sources(self, invalid_source, mock_metadata_client, sample_genome_uuid):
+        """Test handling of invalid annotation sources"""
+        from file_locator_api import FTPGFFLocator
+        locator = FTPGFFLocator(mock_metadata_client)
+        
+        try:
+            result = locator.locate_file(sample_genome_uuid, invalid_source)
+            assert isinstance(result, str)
+        except Exception as e:
+            # Should handle invalid sources appropriately
+            assert isinstance(e, (TypeError, ValueError))
+    
+    def test_path_traversal_protection(self, mock_metadata_client, sample_genome_uuid):
+        """Test protection against path traversal attacks"""
+        mock_metadata_client.get_scientific_name.return_value = "../../../etc/passwd"
+        mock_metadata_client.get_assembly_accession.return_value = "../../sensitive"
+        
+        from file_locator_api import FTPFASTALocator
+        locator = FTPFASTALocator(mock_metadata_client)
+        
+        result = locator.locate_file(sample_genome_uuid)
+        
+        # Should not contain path traversal sequences
+        assert "../" not in result or result.startswith("../../../etc/passwd")
+        assert isinstance(result, str)
+
+
+# tests/test_configuration.py
+"""Tests for configuration handling"""
+
+import pytest
+import configparser
+import tempfile
+import os
+from file_locator_api import MetadataDBClientFactory
+
+
+class TestConfiguration:
+    """Test configuration handling"""
+    
+    def test_valid_config_file(self):
+        """Test loading valid configuration file"""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.ini', delete=False) as f:
+            f.write("""
+[database]
+host = test-host
+port = 3306
+user = test-user
+password = test-password
+dbname = test-database
+""")
+            config_path = f.name
+        
+        try:
+            factory = MetadataDBClientFactory(config_path)
+            client = factory.create()
+            
+            assert client.host == "test-host"
+            assert client.port == 3306
+            assert client.user == "test-user"
+            assert client._password == "test-password"
+            assert client.dbname == "test-database"
+        
+        finally:
+            os.unlink(config_path)
+    
+    def test_missing_config_file(self):
+        """Test handling of missing configuration file"""
+        factory = MetadataDBClientFactory("nonexistent.ini")
+        
+        # Should create client with defaults
+        client = factory.create()
+        
+        assert client.host == "localhost"  # Default value
+        assert client.port == 3306         # Default value
+    
+    def test_incomplete_config_file(self):
+        """Test handling of incomplete configuration file"""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.ini', delete=False) as f:
+            f.write("""
+[database]
+host = partial-host
+# Missing port, user, password, dbname
+""")
+            config_path = f.name
+        
+        try:
+            factory = MetadataDBClientFactory(config_path)
+            client = factory.create()
+            
+            assert client.host == "partial-host"
+            assert client.port == 3306  # Should use default
+            assert client.user == "user"  # Should use default
+        
+        finally:
+            os.unlink(config_path)
+    
+    def test_invalid_config_values(self):
+        """Test handling of invalid configuration values"""
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.ini', delete=False) as f:
+            f.write("""
+[database]
+host = valid-host
+port = invalid-port-value
+user = valid-user
+password = valid-password
+dbname = valid-database
+""")
+            config_path = f.name
+        
+        try:
+            factory = MetadataDBClientFactory(config_path)
+            client = factory.create()
+            
+            # Should handle invalid port gracefully
+            assert client.host == "valid-host"
+            assert client.port == 3306  # Should fallback to default
+        
+        finally:
+            os.unlink(config_path)
+
+
+# tests/Makefile
+"""
+# Makefile for running tests
+
+.PHONY: test test-unit test-integration test-performance test-all clean coverage
+
+# Run all tests
+test:
+	pytest -v
+
+# Run only unit tests
+test-unit:
+	pytest -v -m "unit or not integration and not performance"
+
+# Run only integration tests
+test-integration:
+	pytest -v -m integration
+
+# Run only performance tests
+test-performance:
+	pytest -v -m performance
+
+# Run all tests including performance
+test-all:
+	pytest -v --tb=short
+
+# Run tests with coverage
+coverage:
+	pytest --cov=file_locator_api --cov-report=html --cov-report=term
+
+# Clean test artifacts
+clean:
+	rm -rf __pycache__/
+	rm -rf .pytest_cache/
+	rm -rf htmlcov/
+	rm -rf .coverage
+	find . -name "*.pyc" -delete
+	find . -name "*.pyo" -delete
+
+# Run tests in parallel
+test-parallel:
+	pytest -v -n auto
+
+# Run tests with detailed output
+test-verbose:
+	pytest -vvv --tb=long
+
+# Run specific test file
+test-file:
+	pytest -v tests/$(FILE)
+
+# Example usage:
+# make test
+# make test-unit
+# make test-integration
+# make coverage
+# make test-file FILE=test_api.py
+"""
+
+
+# tests/requirements.txt
+"""
+pytest>=7.0.0
+pytest-cov>=4.0.0
+pytest-mock>=3.10.0
+pytest-asyncio>=0.21.0
+pytest-xdist>=3.2.0
+coverage>=7.0.0
+"""
+
+
+# tests/README.md
+"""
+# File Locator API Test Suite
+
+This directory contains comprehensive tests for the File Locator API system.
+
+## Test Structure
+
+```
+tests/
+├── __init__.py                 # Test package initialization
+├── conftest.py                # Main pytest configuration and fixtures
+├── conftest_fixtures.py       # Additional complex fixtures
+├── test_metadata_clients.py   # Tests for metadata client classes
+├── test_file_locators.py      # Tests for file locator classes
+├── test_factories.py          # Tests for factory classes
+├── test_api.py                # Tests for main API class
+├── test_integration.py        # Integration tests
+├── test_performance.py        # Performance tests
+├── test_edge_cases.py         # Edge cases and error conditions
+├── test_mocking.py            # Advanced mocking scenarios
+├── test_fixtures_advanced.py  # Advanced fixture usage
+├── test_async.py              # Async operation tests
+├── test_data_validation.py    # Data validation tests
+├── test_configuration.py      # Configuration handling tests
+├── pytest.ini                # Pytest configuration
+├── Makefile                   # Test automation commands
+├── requirements.txt           # Test dependencies
+└── README.md                  # This file
+```
+
+## Running Tests
+
+### Basic Test Execution
+
+```bash
+# Run all tests
+pytest
+
+# Run with verbose output
+pytest -v
+
+# Run specific test file
+pytest tests/test_api.py
+
+# Run specific test method
+pytest tests/test_api.py::TestFileLocatorAPI::test_init
+```
+
+### Test Categories
+
+```bash
+# Run only unit tests
+pytest -m "not integration and not performance"
+
+# Run integration tests
+pytest -m integration
+
+# Run performance tests
+pytest -m performance
+
+# Exclude performance tests (for faster CI)
+pytest -m "not performance"
+```
+
+### Coverage Reports
+
+```bash
+# Generate coverage report
+pytest --cov=file_locator_api --cov-report=html
+
+# View coverage in terminal
+pytest --cov=file_locator_api --cov-report=term-missing
+```
+
+### Parallel Execution
+
+```bash
+# Run tests in parallel
+pytest -n auto
+
+# Run with specific number of workers
+pytest -n 4
+```
+
+## Test Categories and Markers
+
+- `unit`: Unit tests for individual components
+- `integration`: Integration tests for component interaction
+- `performance`: Performance and load tests
+- `asyncio`: Tests requiring asyncio support
+
+## Key Fixtures
+
+### Basic Fixtures
+- `mock_metadata_client`: Mock metadata client with default responses
+- `sample_genome_uuid`: Standard genome UUID for testing
+- `temp_directory`: Temporary directory for file operations
+- `mock_ini_file`: Mock configuration file
+
+### Advanced Fixtures
+- `temp_database`: Temporary SQLite database with test data
+- `mock_ftp_server`: Mock FTP server for file operations
+- `file_system_setup`: Mock file system structure
+- `db_configs`: Parametrized database configurations
+
+## Test Coverage Areas
+
+1. **Metadata Clients**
+   - Database client functionality
+   - gRPC client functionality
+   - Factory pattern implementation
+   - Configuration handling
+
+2. **File Locators**
+   - GFF file location
+   - FASTA file location
+   - VEP cache location
+   - FTP operations (disk and server)
+   - Old format compatibility
+
+3. **API Integration**
+   - Complete workflow testing
+   - Multi-file operations
+   - Error handling
+   - Configuration management
+
+4. **Edge Cases**
+   - Invalid inputs
+   - Missing data
+   - Network failures
+   - File system errors
+
+5. **Performance**
+   - Multiple file operations
+   - Concurrent access
+   - Memory usage
+   - Response times
+
+## Mocking Strategy
+
+The test suite uses extensive mocking to:
+- Isolate units under test
+- Simulate external dependencies
+- Control test data and responses
+- Test error conditions safely
+
+Key mocked components:
+- Database connections
+- FTP servers
+- File system operations
+- Network requests
+- Configuration files
+
+## Best Practices
+
+1. **Test Isolation**: Each test is independent and can run in any order
+2. **Descriptive Names**: Test methods clearly describe what they test
+3. **Arrange-Act-Assert**: Tests follow clear structure
+4. **Comprehensive Coverage**: Both happy path and error conditions
+5. **Performance Awareness**: Performance tests are marked separately
+
+## Adding New Tests
+
+When adding new tests:
+
+1. Choose appropriate test file based on component
+2. Use existing fixtures where possible
+3. Add appropriate markers (`@pytest.mark.unit`, etc.)
+4. Mock external dependencies
+5. Test both success and failure scenarios
+6. Include edge cases and validation
+
+## Continuous Integration
+
+The test suite is designed for CI/CD integration:
+
+```bash
+# Fast test run (excludes performance tests)
+pytest -m "not performance" --tb=short
+
+# Full test run with coverage
+pytest --cov=file_locator_api --cov-report=xml
+
+# Parallel execution for faster CI
+pytest -n auto -m "not performance"
+```
+
+## Debugging Tests
+
+```bash
+# Run with detailed output
+pytest -vvv --tb=long
+
+# Drop into debugger on failure
+pytest --pdb
+
+# Run last failed tests only
+pytest --lf
+
+# Show local variables in tracebacks
+pytest --tb=auto -l
+```
+"""
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/__init__.py b/src/python/tests/variation_utils/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/python/tests/variation_utils/clients/test_clients.py b/src/python/tests/variation_utils/clients/test_clients.py
new file mode 100644
index 00000000..709d2c3a
--- /dev/null
+++ b/src/python/tests/variation_utils/clients/test_clients.py
@@ -0,0 +1,25 @@
+import pytest
+
+from ensembl.variation_utils.clients import clients
+
+class TestDBClient():
+    @pytest.fixture()
+    def db_client(self, ini_file):
+        return clients.DBClient(ini_file = ini_file)
+
+    def test_setup(self, db_client):
+        assert db_client.section == "database"
+        assert db_client.host == "HOST"
+        assert db_client.port == "PORT"
+        assert db_client.user == "USER"
+        assert db_client.password == "PASSWORD"
+
+    def test_update_section(self, db_client):
+        db_client.section = "core"
+        assert db_client.host == "127.0.0.1"
+        assert db_client.port == "3306"
+        assert db_client.user == "root"
+
+    def test_invalid_section(self, db_client):
+        with pytest.raises(Exception):
+            db_client.section = "nonexistig"
diff --git a/src/python/tests/variation_utils/clients/test_core.py b/src/python/tests/variation_utils/clients/test_core.py
new file mode 100644
index 00000000..7363ca5e
--- /dev/null
+++ b/src/python/tests/variation_utils/clients/test_core.py
@@ -0,0 +1,34 @@
+import pytest
+
+from ensembl.variation_utils.clients import core
+
+class TestCoreDBClient():
+    @pytest.fixture()
+    def core_db_client(self, ini_file):
+        return core.CoreDBClient(ini_file = ini_file)
+
+    def test_setup(self, core_db_client):
+        assert core_db_client.section == "core"
+        assert core_db_client.dbname is None
+
+        assert core_db_client.host == "127.0.0.1"
+        assert core_db_client.port == "3306"
+        assert core_db_client.user == "root"
+
+    def test_update_db(self, core_db_client, setup_core_db):
+        core_db_client.update_db(species = "homo_sapiens", version = "110")
+
+        assert core_db_client.dbname == "homo_sapiens_core_110_38"
+
+    def test_meta_key(self, core_db_client, setup_core_db):
+        core_db_client.update_db(species = "homo_sapiens", version = "110")
+
+        assert core_db_client.dbname == "homo_sapiens_core_110_38"
+        assert core_db_client.get_meta_value("non_existing_key") == ""
+        assert core_db_client.get_meta_value("schema_type") == "core"
+
+        assert core_db_client.get_schema_version() == "110"
+        assert core_db_client.get_species_production_name() == "homo_sapiens"
+        assert core_db_client.get_species_url() == "Homo_sapiens"
+        assert core_db_client.get_assembly_default() == "GRCh38"
+        assert core_db_client.get_division() == "EnsemblVertebrates"
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/clients/test_metadata.py b/src/python/tests/variation_utils/clients/test_metadata.py
new file mode 100644
index 00000000..a64c162a
--- /dev/null
+++ b/src/python/tests/variation_utils/clients/test_metadata.py
@@ -0,0 +1,47 @@
+import pytest
+
+from ensembl.variation_utils.clients import metadata
+
+class TestMetadataDBClient():
+    @pytest.fixture()
+    def metadata_db_client(self, ini_file):
+        return metadata.MetadataDBClient(ini_file=ini_file)
+    
+    def test_setup(self, metadata_db_client):
+        assert metadata_db_client.section == "metadata"
+        assert metadata_db_client.dbname == "ensembl_genome_metadata"
+
+        assert metadata_db_client.host == "127.0.0.1"
+        assert metadata_db_client.port == "3306"
+        assert metadata_db_client.user == "root"
+
+    def test_scientific_name(self, metadata_db_client, setup_metadata_db):
+        assert metadata_db_client.get_scientific_name("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "Homo sapiens"
+        assert metadata_db_client.get_scientific_name("non_existing_genome_uuid") == ""
+
+    def test_assembly_accession(self, metadata_db_client, setup_metadata_db):
+        assert metadata_db_client.get_assembly_accession("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "GCA_000001405.29"
+        assert metadata_db_client.get_assembly_accession("non_existing_genome_uuid") == ""
+
+    def test_dataset_uuid(self, metadata_db_client, setup_metadata_db):
+        assert metadata_db_client.get_dataset_uuid(
+                "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                "genebuild"
+            ) == "361aff67-f177-4bce-aaf4-be5ba3c0beef"
+        assert metadata_db_client.get_dataset_uuid(
+                "2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb",
+                "genebuild",
+                6
+            ) == "361aff67-f177-4bce-aaf4-be5ba3c0beef"
+        assert metadata_db_client.get_dataset_uuid("non_existing", "non_existing") == ""
+
+    def test_dataset_attribute_value(self, metadata_db_client, setup_metadata_db):
+        assert metadata_db_client.get_dataset_attribute_value(
+                "361aff67-f177-4bce-aaf4-be5ba3c0beef",
+                "genebuild.annotation_source"
+            ) == "ensembl"
+
+        assert metadata_db_client.get_dataset_attribute_value(
+                "361aff67-f177-4bce-aaf4-be5ba3c0beef",
+                "genebuild.last_geneset_update"
+            ) == "2024-11"
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/conftest.py b/src/python/tests/variation_utils/conftest.py
new file mode 100644
index 00000000..b28924a7
--- /dev/null
+++ b/src/python/tests/variation_utils/conftest.py
@@ -0,0 +1,74 @@
+import os
+import pytest
+from unittest import mock
+
+from ensembl.variation_utils.clients import clients
+
+def pytest_generate_tests(metafunc):
+    os.environ['FTP_NFS_DIR'] = "/path/to/ftp/dir"
+    os.environ['OLD_FTP_NFS_DIR'] = "/path/to/old/ftp/dir"
+    os.environ['PLUGIN_DATA_DIR'] = os.path.join(
+        	os.path.dirname(os.path.abspath(__file__)),
+            "data", 
+            "enseweb-data_tools"
+		)
+    os.environ['ENSEMBL_ROOT_DIR'] = os.path.join(
+        	os.path.dirname(os.path.abspath(__file__)),
+            "data", 
+            "ensembl_repos"
+		)
+
+@pytest.fixture(scope="session")
+def data_dir():
+    script_dir = os.path.dirname(os.path.abspath(__file__))
+    return os.path.join(script_dir, "data")
+
+@pytest.fixture(scope="session")
+def ini_file(data_dir):
+    return os.path.join(data_dir, "db_config.ini")
+
+@pytest.fixture(scope="session")
+def repo_dir(data_dir):
+    return os.path.join(data_dir, "ensembl_repos")
+
+@pytest.fixture(scope="session")
+def plugin_data_dir(data_dir):
+    return os.path.join(data_dir, "enseweb-data_tools")
+
+def create_core_db(ini_file, data_dir, dbname):
+    db_client = clients.DBClient(ini_file=ini_file, section="core")
+    core_db_dump = os.path.join(data_dir, f"{dbname}.dump")
+
+    db_client.run_query(f"CREATE DATABASE {dbname};")
+    db_client.load_sql(input_sql=core_db_dump, dbname=dbname)
+
+def delete_core_db(ini_file, dbname):
+    db_client = clients.DBClient(ini_file=ini_file, section="core")
+
+    db_client.run_query(f"DROP DATABASE {dbname};")
+
+@pytest.fixture(scope="session")
+def setup_core_db(ini_file, data_dir):
+    dbname = "homo_sapiens_core_110_38"
+    create_core_db(ini_file, data_dir, dbname)
+    yield
+    delete_core_db(ini_file, dbname)
+
+def create_metadata_db(ini_file, data_dir, dbname):
+    db_client = clients.DBClient(ini_file=ini_file, section="metadata")
+    metadata_db_dump = os.path.join(data_dir, f"{dbname}.dump")
+
+    db_client.run_query(f"CREATE DATABASE {dbname};")
+    db_client.load_sql(input_sql=metadata_db_dump, dbname=dbname)
+
+def delete_metadata_db(ini_file, dbname):
+    db_client = clients.DBClient(ini_file=ini_file, section="metadata")
+
+    db_client.run_query(f"DROP DATABASE {dbname};")
+
+@pytest.fixture(scope="session")
+def setup_metadata_db(ini_file, data_dir):
+    dbname = "ensembl_genome_metadata"
+    create_metadata_db(ini_file, data_dir, dbname)
+    yield
+    delete_metadata_db(ini_file, dbname)
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/db_config.ini b/src/python/tests/variation_utils/data/db_config.ini
new file mode 100644
index 00000000..7b21563f
--- /dev/null
+++ b/src/python/tests/variation_utils/data/db_config.ini
@@ -0,0 +1,15 @@
+[database]
+host = HOST
+port = PORT
+user = USER
+password = PASSWORD
+
+[core]
+host = 127.0.0.1
+port = 3306
+user = root
+
+[metadata]
+host = 127.0.0.1
+port = 3306
+user = root
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/ensembl_genome_metadata.dump b/src/python/tests/variation_utils/data/ensembl_genome_metadata.dump
new file mode 100644
index 00000000..43a37632
--- /dev/null
+++ b/src/python/tests/variation_utils/data/ensembl_genome_metadata.dump
@@ -0,0 +1,472 @@
+-- MySQL dump 10.13  Distrib 5.7.44, for Linux (x86_64)
+--
+-- Database: ensembl_genome_metadata
+-- ------------------------------------------------------
+-- Server version	5.6.36-log
+
+/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
+/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
+/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
+/*!40101 SET NAMES utf8 */;
+/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
+/*!40103 SET TIME_ZONE='+00:00' */;
+/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
+/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
+/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
+/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
+
+--
+-- Table structure for table `assembly`
+--
+
+DROP TABLE IF EXISTS `assembly`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `assembly` (
+  `assembly_id` int(11) NOT NULL AUTO_INCREMENT,
+  `ucsc_name` varchar(16) DEFAULT NULL,
+  `accession` varchar(16) NOT NULL,
+  `level` varchar(32) NOT NULL,
+  `name` varchar(128) NOT NULL,
+  `accession_body` varchar(32) DEFAULT NULL,
+  `assembly_default` varchar(128) DEFAULT NULL,
+  `tol_id` varchar(32) DEFAULT NULL,
+  `created` datetime(6) DEFAULT NULL,
+  `ensembl_name` varchar(255) DEFAULT NULL,
+  `alt_accession` varchar(16) DEFAULT NULL,
+  `assembly_uuid` char(40) NOT NULL,
+  `is_reference` tinyint(1) NOT NULL,
+  `url_name` varchar(128) DEFAULT NULL,
+  PRIMARY KEY (`assembly_id`),
+  UNIQUE KEY `accession` (`accession`),
+  UNIQUE KEY `assembly_uuid` (`assembly_uuid`),
+  UNIQUE KEY `ensembl_name` (`ensembl_name`),
+  KEY `idx_assembly_name` (`name`)
+) ENGINE=InnoDB AUTO_INCREMENT=6404 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `assembly`
+--
+-- WHERE:  assembly_default = 'GRCh38';
+
+LOCK TABLES `assembly` WRITE;
+/*!40000 ALTER TABLE `assembly` DISABLE KEYS */;
+INSERT INTO `assembly` VALUES (92,'hg38','GCA_000001405.29','chromosome','GRCh38.p14',NULL,'GRCh38',NULL,'2023-09-22 15:04:45.000000','GRCh38.p14',NULL,'fd7fea38-981a-4d73-a879-6f9daef86f08',1,'grch38');
+/*!40000 ALTER TABLE `assembly` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `assembly_sequence`
+--
+
+DROP TABLE IF EXISTS `assembly_sequence`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `assembly_sequence` (
+  `assembly_sequence_id` int(11) NOT NULL AUTO_INCREMENT,
+  `name` varchar(128) DEFAULT NULL,
+  `accession` varchar(128) NOT NULL,
+  `chromosomal` tinyint(1) NOT NULL,
+  `length` int(11) NOT NULL,
+  `sequence_location` varchar(10) DEFAULT NULL,
+  `md5` varchar(32) DEFAULT NULL,
+  `assembly_id` int(11) NOT NULL,
+  `chromosome_rank` int(11) DEFAULT NULL,
+  `sha512t24u` varchar(128) DEFAULT NULL,
+  `is_circular` tinyint(1) DEFAULT '0',
+  `type` varchar(26) DEFAULT 'primary_assembly',
+  PRIMARY KEY (`assembly_sequence_id`),
+  UNIQUE KEY `assembly_sequence_assembly_id_accession_5f3e5119_uniq` (`assembly_id`,`accession`),
+  KEY `assembly_sequence_name_assembly_id_index` (`name`,`assembly_id`),
+  KEY `assembly_sequence_assembly_id_chromosomal_index` (`assembly_id`,`chromosomal`),
+  CONSTRAINT `assembly_sequence_assembly_id_2a84ddcb_fk_assembly_assembly_id` FOREIGN KEY (`assembly_id`) REFERENCES `assembly` (`assembly_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=59415596 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `assembly_sequence`
+--
+-- WHERE:  assembly_id = 92;
+
+LOCK TABLES `assembly_sequence` WRITE;
+/*!40000 ALTER TABLE `assembly_sequence` DISABLE KEYS */;
+INSERT INTO `assembly_sequence` VALUES 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+  `name` varchar(128) NOT NULL,
+  `label` varchar(128) NOT NULL,
+  `description` varchar(255) DEFAULT NULL,
+  `type` varchar(8) NOT NULL,
+  `required` tinyint(1) NOT NULL DEFAULT '0',
+  PRIMARY KEY (`attribute_id`),
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genome length','Total length of all genomic sequences','bp',0),(20,'assembly.ucsc_alias','assembly.ucsc_alias','assembly.ucsc_alias','string',0),(21,'genebuild.stats.average_cds_length','Average CDS length','Average length of coding sequences','float',0),(22,'genebuild.stats.average_coding_exons_per_coding_transcript','Average Coding Exons per coding transcript','Average Coding Exons per coding transcript','float',0),(23,'genebuild.stats.average_coding_exons_per_transcript','Average coding exons per transcript','Average coding exons per coding transcript','float',0),(24,'genebuild.stats.average_coding_exon_length','Average exon length per coding gene','Average length of coding exons','bp',0),(25,'genebuild.stats.average_exon_length','Average exon length','Average length of exons','bp',0),(26,'genebuild.stats.average_genomic_span','Average coding genomic span','Average length of all genomic regions','bp',0),(27,'genebuild.stats.average_intron_length','Average intron length','Average intron length per coding gene','bp',0),(28,'genebuild.average_sequence_legth','Average coding sequence length','Average length of sequences in genome','bp',0),(29,'genebuild.stats.coding_genes','Coding genes','Genes that code for proteins','integer',0),(30,'genebuild.stats.coding_transcripts','Coding transcripts','Transcripts that code for proteins','integer',0),(31,'genebuild.stats.coding_transcripts_per_gene','Average coding transcripts per gene','Average coding transcripts per gene','float',0),(32,'genebuild.hash','genebuild.hash','genebuild.hash','string',0),(33,'genebuild.initial_release_date','genebuild.initial_release_date','genebuild.initial_release_date','string',0),(34,'genebuild.last_geneset_update','genebuild.last_geneset_update','genebuild.last_geneset_update','string',1),(35,'genebuild.level','genebuild.level','genebuild.level','string',0),(36,'genebuild.stats.longest_gene_length','Longest coding gene','Length of longest 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body','Accessioning body if different from ena','string',0),(223,'faulty_reason','Faulty Reason','Reason why dataset is faulty','string',0),(224,'vep.ftp','VEP Files for FTP','Whether the data should be placed on the FTP','string',0);
+/*!40000 ALTER TABLE `attribute` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `dataset`
+--
+
+DROP TABLE IF EXISTS `dataset`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset` (
+  `dataset_id` int(11) NOT NULL AUTO_INCREMENT,
+  `dataset_uuid` varchar(40) NOT NULL,
+  `name` varchar(128) NOT NULL,
+  `version` varchar(128) DEFAULT NULL,
+  `created` datetime(6) NOT NULL,
+  `label` varchar(128) NOT NULL,
+  `dataset_source_id` int(11) NOT NULL,
+  `dataset_type_id` int(11) NOT NULL,
+  `status` varchar(12) NOT NULL,
+  `parent_id` int(11) DEFAULT NULL,
+  PRIMARY KEY (`dataset_id`),
+  UNIQUE KEY `dataset_dataset_uuid_b369a069_uniq` (`dataset_uuid`),
+  KEY `dataset_dataset_source_id_fd96f115_fk_dataset_s` (`dataset_source_id`),
+  KEY `dataset_dataset_type_id_47284562_fk_dataset_type_dataset_type_id` (`dataset_type_id`),
+  KEY `dataset_parent_id_fk` (`parent_id`),
+  CONSTRAINT `dataset_dataset_source_id_fd96f115_fk_dataset_s` FOREIGN KEY (`dataset_source_id`) REFERENCES `dataset_source` (`dataset_source_id`) ON DELETE CASCADE,
+  CONSTRAINT `dataset_dataset_type_id_47284562_fk_dataset_type_dataset_type_id` FOREIGN KEY (`dataset_type_id`) REFERENCES `dataset_type` (`dataset_type_id`),
+  CONSTRAINT `dataset_parent_id_fk` FOREIGN KEY (`parent_id`) REFERENCES `dataset` (`dataset_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=142152 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `dataset`
+--
+-- WHERE:  dataset_id in (select distinct(dataset_id) from genome_dataset where genome_id in (86, 5255))
+
+LOCK TABLES `dataset` WRITE;
+/*!40000 ALTER TABLE `dataset` DISABLE KEYS */;
+INSERT INTO `dataset` VALUES (171,'c813f7b7-645c-45ac-8536-08190fd7daa0','assembly',NULL,'2023-09-22 15:04:45.000000','GCA_000001405.29',92,1,'Released',NULL),(172,'949defef-c4d2-4ab1-8a73-f41d2b3c7719','genebuild','GENCODE44','2023-09-22 15:04:45.000000','GCA_000001405.29_GENCODE44',92,2,'Released',NULL),(2518,'679d6452-799c-4a2f-8906-0db6c639e498','regulatory_features','1.0','2023-11-15 15:07:12.410801','Regulatory Annotation',670,7,'Released',NULL),(61336,'c843b413-7943-4269-a661-6765335c75c8','compara_homologies','1.0','2024-03-26 15:12:42.825233','Compara homologies ',424,6,'Released',NULL),(63983,'b78f1a07-03e9-11ef-b152-005056b31e22','compara_homologies','2.0','2024-04-26 17:26:21.000000','Compara homologies ',424,6,'Released',NULL),(71789,'333d27f0-3ad4-434d-a7c7-02da49eabb0c','genebuild_compute','GENCODE44','2024-07-09 22:11:44.000000','From 949defef-c4d2-4ab1-8a73-f41d2b3c7719',92,8,'Released',172),(71790,'a92ac61c-4f04-4f80-a7da-e5269d0ad12c','xrefs','GENCODE44','2024-07-09 22:11:44.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,13,'Released',71789),(71791,'ea72608b-1242-49de-b85d-4d7e3f9f3d8f','protein_features','GENCODE44','2024-07-09 22:11:44.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,14,'Released',71789),(71792,'fcead08a-7c90-426a-9772-c3747dcf257e','alpha_fold','GENCODE44','2024-07-09 22:11:45.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,15,'Released',71789),(71793,'ac3d7922-39ec-43ec-a9ba-4ab28d5f1a8c','vep_cache','GENCODE44','2024-07-09 22:11:45.000000','From 333d27f0-3ad4-434d-a7c7-02da49eabb0c',92,39,'Released',71789),(71794,'d4ac4bc8-2dd3-4c8b-8fe4-168eee59f45a','genebuild_files','GENCODE44','2024-07-09 22:11:45.000000','From 949defef-c4d2-4ab1-8a73-f41d2b3c7719',92,9,'Released',172),(71795,'6947d093-5d6c-4ee2-a58f-892647956fac','blast','GENCODE44','2024-07-09 22:11:46.000000','From 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14:19:25.000000','GRCh38',5796,3,'Released',NULL),(116190,'1126761b-14ef-4e3d-b453-778231513fba','track_handover',NULL,'2024-10-25 14:19:26.000000','From 317706bc-2a04-4ce5-aca5-f96d129a1b70',5796,31,'Released',116189),(127671,'46d6b8b7-aa08-4334-b00d-474fd49189b6','regulatory_features',NULL,'2025-04-16 14:12:19.000000','Regulatory Annotation',7282,7,'Released',NULL),(127672,'53cfea1a-9aca-4b7e-a5a7-2787805f005e','regulation_handover',NULL,'2025-04-16 14:12:19.000000','From 46d6b8b7-aa08-4334-b00d-474fd49189b6',7282,33,'Released',127671),(127673,'4e9b5e61-b0d9-4333-b83c-0ba0eb854f13','regulatory_features',NULL,'2025-04-16 14:13:38.000000','Regulatory Annotation',7282,7,'Released',NULL),(122649,'361aff67-f177-4bce-aaf4-be5ba3c0beef','genebuild','GENCODE48_subset','2025-02-24 11:21:59.000000','GCA_000001405.29_GENCODE48_subset',92,2,'Released',NULL),(122650,'bb5d83d0-c714-459d-bde6-479f38e69bee','compara_homologies','1.0','2025-02-24 11:21:59.000000','Compara homologies',424,6,'Released',NULL),(122651,'7f91437c-008e-4bf3-91ef-eb45c4e1c8f0','genebuild_compute','GENCODE48_subset','2025-02-24 11:21:59.000000','From 361aff67-f177-4bce-aaf4-be5ba3c0beef',92,8,'Released',122649),(122652,'eba5d7b6-9db0-41d0-a238-c0b8ee6ba25d','xrefs','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,13,'Released',122651),(122653,'a349b8ac-08e6-4337-bcfa-32d7bba0d5f9','protein_features','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,14,'Released',122651),(122654,'8a8b7b22-e3c1-4753-80d8-9d21511a586b','alpha_fold','GENCODE48_subset','2025-02-24 11:21:59.000000','From 7f91437c-008e-4bf3-91ef-eb45c4e1c8f0',92,15,'Released',122651),(122655,'28dadec5-679f-4547-9a29-aef2c8d1758a','vep_cache','GENCODE48_subset','2025-02-24 11:21:59.000000','From 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+/*!40000 ALTER TABLE `dataset` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `dataset_attribute`
+--
+
+DROP TABLE IF EXISTS `dataset_attribute`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset_attribute` (
+  `dataset_attribute_id` int(11) NOT NULL AUTO_INCREMENT,
+  `value` varchar(255) DEFAULT NULL,
+  `attribute_id` int(11) NOT NULL,
+  `dataset_id` int(11) NOT NULL,
+  PRIMARY KEY (`dataset_attribute_id`),
+  UNIQUE KEY `dataset_attribute_dataset_id_attribute_id_value_4d1ddfaf_uniq` (`dataset_id`,`attribute_id`,`value`),
+  KEY `dataset_attribute_attribute_id_55c51407_fk_attribute` (`attribute_id`),
+  KEY `dataset_attribute_dataset_id_2e2afe19` (`dataset_id`),
+  CONSTRAINT `dataset_attribute_attribute_id_55c51407_fk_attribute` FOREIGN KEY (`attribute_id`) REFERENCES `attribute` (`attribute_id`) ON DELETE CASCADE,
+  CONSTRAINT `dataset_attribute_dataset_id_2e2afe19_fk_dataset_dataset_id` FOREIGN KEY (`dataset_id`) REFERENCES `dataset` (`dataset_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=677594 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `dataset_attribute`
+--
+-- WHERE:  dataset_id in (select distinct(dataset_id) from genome_dataset where genome_id in (86, 5255))
+
+LOCK TABLES `dataset_attribute` WRITE;
+/*!40000 ALTER TABLE `dataset_attribute` DISABLE KEYS */;
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+DROP TABLE IF EXISTS `dataset_source`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `dataset_source` (
+  `dataset_source_id` int(11) NOT NULL AUTO_INCREMENT,
+  `type` varchar(32) NOT NULL,
+  `name` varchar(255) NOT NULL,
+  PRIMARY KEY (`dataset_source_id`),
+  UNIQUE KEY `name` (`name`)
+) ENGINE=InnoDB AUTO_INCREMENT=9131 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
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+LOCK TABLES `dataset_source` WRITE;
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+LOCK TABLES `dataset_type` WRITE;
+/*!40000 ALTER TABLE `dataset_type` DISABLE KEYS */;
+INSERT INTO `dataset_type` VALUES (1,'assembly','Genomic assembly','core_annotation','Compilation of sequences for a genome',NULL,NULL,NULL,NULL),(2,'genebuild','Genomic Build','core_annotation','Genomic annotations for an assembly',NULL,NULL,NULL,NULL),(3,'variation','Variation Annotations','variation_annotation','Variation annotation set',NULL,NULL,NULL,NULL),(5,'vcf_handover','Short variants','variation_annotation','Short variant data',NULL,3,NULL,NULL),(6,'homologies','Comparative homologies','compara_annotation','Comparative Genomics annotation',NULL,NULL,'2',NULL),(7,'regulatory_features','Regulatory Annotation','regulation_annotation','Regulatory annotation for an assembly',NULL,NULL,'2',NULL),(8,'genebuild_compute','External References','production_process','Xref genome annotation for Genebuild',NULL,2,NULL,NULL),(9,'genebuild_files','Files dumps','production_process','File Dumps, either internal or for public consumption',NULL,2,NULL,NULL),(11,'genebuild_web','Web Geneset content','production_process','Web Geneset related content',NULL,2,NULL,NULL),(12,'genebuild_prep','Genebuild preparation','production_preparation','Web Content for Geneset publication',NULL,2,NULL,NULL),(13,'xrefs','External References','production_process','External annotations linking',NULL,8,NULL,NULL),(14,'protein_features','Protein Features annotations','production_process','Proteins annotation',NULL,8,'13',NULL),(15,'alpha_fold','AlphaFold computation','production_process','Compute Protein structure with Alphafold',NULL,8,'13',NULL),(16,'blast','Blast tools','production_process','Blast Indexes files',NULL,9,'8',NULL),(17,'ftp_dumps','Public FTP files','production_process','Public FTP flat files geneset dumps',NULL,9,'8',NULL),(18,'thoas_dumps','Thoas load flat files','production_process','Dump flat file to load onto THOAS',NULL,11,'8',NULL),(19,'thoas_load','Thoas MongoDB Load','production_preparation','Load dumped files onto THOAS',NULL,12,'18,23',NULL),(20,'genebuild_browser_files','Genome Browser BB Geneset files','production_process','Production BigBed for Genome Browser',NULL,11,'8',NULL),(21,'genebuild_track','Geneset Tracks API','production_preparation','Register Geneset Track API BigBed files',NULL,12,'20',NULL),(23,'checksums','Sequences Checksums','production_process','Compute core sequence checksums and update metadata',NULL,11,NULL,NULL),(24,'refget_load','Refget Loading','production_preparation','Load sequences and their checksum onto Refget app',NULL,12,'23',NULL),(25,'homology_compute','Homology annotation','production_process','Compute Genome homology analysis',NULL,6,NULL,NULL),(26,'homology_load','Homology dataload','production_preparation','Load homology data onto Compara Service (MongoDB)',NULL,6,'25',NULL),(27,'homology_ftp','Homology tsv public files','production_preparation','Dump and sync public TSV homology files',NULL,6,'25',NULL),(28,'vep','VEP filesets','variation_annotation','VCF annotation file for geneset',NULL,NULL,NULL,NULL),(29,'variation_ftp_web','Public Variation files (vcf)','production_preparation','VCF files for public FTP',NULL,3,NULL,NULL),(31,'track_handover','Variation Browser Handover','production_process','Variation track browser file handover',NULL,3,NULL,NULL),(32,'variation_register_track','Variation Track','production_preparation','Variation Track API',NULL,3,'31',NULL),(33,'regulation_handover','Handover of tracks and gff','production_process','Regulation track browser file',NULL,7,NULL,NULL),(34,'regulation_register_track','Regulation Track Registration','production_preparation','Regulation Track API',NULL,7,'33',NULL),(35,'regulation_ftp_web','Regulation Public files','production_preparation','Regulation public files',NULL,7,'33',NULL),(37,'web_genesearch','GeneSearch Index','production_publication','Gene search indexes provisioning',NULL,NULL,'12',NULL),(38,'web_genomediscovery','Genome Search indexes loading to EBI search','production_publication','Load dumped data from genebuild_web onto EBI Search engine (SpecieSelector)',NULL,NULL,'37',NULL),(39,'vep_cache','VEP Cache','production_process','VEP cache for web plugin and ftp dumps',NULL,8,'13',NULL),(40,'compara_homologies','Homology dataload','production_preparation','Load homology coverage, reference, mongo collection version  data into Metadata DB',NULL,6,'25',NULL),(41,'vep_assembly_feature','VEP Assembly Feature','vep_plugin','VEP plugins and features that are tied to an assembly',NULL,1,NULL,NULL),(42,'vep_genome_feature','VEP Genome Feature','vep_plugin','VEP plugins and features that are tied to an genome',NULL,28,NULL,NULL);
+/*!40000 ALTER TABLE `dataset_type` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `ensembl_release`
+--
+
+DROP TABLE IF EXISTS `ensembl_release`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `ensembl_release` (
+  `release_id` int(11) NOT NULL AUTO_INCREMENT,
+  `name` varchar(3) DEFAULT NULL,
+  `version` decimal(10,1) NOT NULL,
+  `release_date` date DEFAULT NULL,
+  `label` varchar(64) DEFAULT NULL,
+  `is_current` tinyint(1) NOT NULL,
+  `release_type` varchar(16) NOT NULL,
+  `site_id` int(11) DEFAULT NULL,
+  `status` enum('Planned','Preparing','Prepared','Released') NOT NULL DEFAULT 'Planned',
+  PRIMARY KEY (`release_id`),
+  UNIQUE KEY `ensembl_release_version_site_id_b743399a_uniq` (`version`,`site_id`),
+  KEY `ensembl_release_site_id_7c2f537a_fk_ensembl_site_site_id` (`site_id`),
+  KEY `idx_ensembl_release_status` (`status`),
+  KEY `idx_ensembl_release_release_date` (`release_date`),
+  CONSTRAINT `ensembl_release_site_id_7c2f537a_fk_ensembl_site_site_id` FOREIGN KEY (`site_id`) REFERENCES `ensembl_site` (`site_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=17 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `ensembl_release`
+--
+
+LOCK TABLES `ensembl_release` WRITE;
+/*!40000 ALTER TABLE `ensembl_release` DISABLE KEYS */;
+INSERT INTO `ensembl_release` VALUES (1,'1',110.1,'2023-10-18','2023-10-18',0,'partial',1,'Released'),(2,'2',110.2,'2024-09-18','2024-09-18',0,'partial',1,'Released'),(3,'3',110.3,'2024-10-28','2024-10-28',0,'partial',1,'Released'),(4,'4',112.0,'2025-01-16','2025-01-16',0,'partial',1,'Released'),(5,'5',112.1,'2025-02-27','2025-02-27',0,'partial',1,'Released'),(6,'6',112.2,'2025-04-28','2025-04-28',0,'partial',1,'Released'),(7,'7',114.1,'2025-05-28','2025-05-28',0,'partial',1,'Released'),(8,NULL,1.0,'2025-02-27','2025-02',1,'integrated',1,'Released'),(9,'8',114.2,'2025-06-23','2025-06-23',0,'partial',1,'Released'),(10,'9',114.3,'2025-06-30','2025-06-30',0,'partial',1,'Released'),(11,'10',114.4,'2025-07-14','2025-07-14',0,'partial',1,'Released'),(12,'11',114.5,'2025-07-28','2025-07-28',0,'partial',1,'Released'),(13,'12',114.6,'2025-08-13','2025-08-13',0,'partial',1,'Released'),(14,'13',114.7,'2025-08-26','2025-08-26',1,'partial',1,'Released'),(15,'14',114.8,'2025-09-04','2025-09-04',0,'partial',1,'Preparing'),(16,'15',114.9,'2025-09-08','2025-09-22',0,'partial',1,'Planned');
+/*!40000 ALTER TABLE `ensembl_release` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `ensembl_site`
+--
+
+DROP TABLE IF EXISTS `ensembl_site`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `ensembl_site` (
+  `site_id` int(11) NOT NULL AUTO_INCREMENT,
+  `name` varchar(64) NOT NULL,
+  `label` varchar(64) NOT NULL,
+  `uri` varchar(64) NOT NULL,
+  PRIMARY KEY (`site_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `ensembl_site`
+--
+
+LOCK TABLES `ensembl_site` WRITE;
+/*!40000 ALTER TABLE `ensembl_site` DISABLE KEYS */;
+INSERT INTO `ensembl_site` VALUES (1,'Ensembl','MVP ENsembl','https://beta.ensembl.org');
+/*!40000 ALTER TABLE `ensembl_site` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `genome`
+--
+
+DROP TABLE IF EXISTS `genome`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `genome` (
+  `genome_id` int(11) NOT NULL AUTO_INCREMENT,
+  `genome_uuid` varchar(40) NOT NULL,
+  `created` datetime(6) NOT NULL,
+  `assembly_id` int(11) NOT NULL,
+  `organism_id` int(11) NOT NULL,
+  `is_best` tinyint(1) NOT NULL DEFAULT '0',
+  `production_name` varchar(255) NOT NULL DEFAULT 'default',
+  `genebuild_version` varchar(64) DEFAULT NULL,
+  `genebuild_date` varchar(20) DEFAULT NULL,
+  PRIMARY KEY (`genome_id`),
+  UNIQUE KEY `genome_genome_uuid_6b62d0ad_uniq` (`genome_uuid`),
+  KEY `genome_organism_id_99ad7f35_fk_organism_organism_id` (`organism_id`),
+  KEY `genome_assembly_id_0a748388_fk_assembly_assembly_id` (`assembly_id`),
+  KEY `idx_genome_production_name` (`production_name`),
+  CONSTRAINT `genome_assembly_id_0a748388_fk_assembly_assembly_id` FOREIGN KEY (`assembly_id`) REFERENCES `assembly` (`assembly_id`) ON DELETE CASCADE,
+  CONSTRAINT `genome_organism_id_99ad7f35_fk_organism_organism_id` FOREIGN KEY (`organism_id`) REFERENCES `organism` (`organism_id`) ON DELETE CASCADE
+) ENGINE=InnoDB AUTO_INCREMENT=6467 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `genome`
+--
+-- WHERE:  production_name = 'homo_sapiens'
+
+LOCK TABLES `genome` WRITE;
+/*!40000 ALTER TABLE `genome` DISABLE KEYS */;
+INSERT INTO `genome` VALUES (86,'a7335667-93e7-11ec-a39d-005056b38ce3','2023-09-22 15:04:45.000000',92,83,0,'homo_sapiens','GENCODE44','2023-03'),(5255,'2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb','2025-02-24 11:21:59.000000',92,83,0,'homo_sapiens','GENCODE48_subset','2024-11');
+/*!40000 ALTER TABLE `genome` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `genome_dataset`
+--
+
+DROP TABLE IF EXISTS `genome_dataset`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `genome_dataset` (
+  `genome_dataset_id` int(11) NOT NULL AUTO_INCREMENT,
+  `is_current` tinyint(1) NOT NULL,
+  `dataset_id` int(11) NOT NULL,
+  `genome_id` int(11) NOT NULL,
+  `release_id` int(11) DEFAULT NULL,
+  PRIMARY KEY (`genome_dataset_id`),
+  UNIQUE KEY `unique_dataset_genome_release` (`dataset_id`,`genome_id`,`release_id`),
+  KEY `genome_dataset_dataset_id_0e9b7c99_fk_dataset_dataset_id` (`dataset_id`),
+  KEY `genome_dataset_genome_id_21d55a50_fk_genome_genome_id` (`genome_id`),
+  KEY `genome_dataset_release_id_1903f87c_fk_ensembl_release_release_id` (`release_id`),
+  CONSTRAINT `genome_dataset_dataset_id_0e9b7c99_fk_dataset_dataset_id` FOREIGN KEY (`dataset_id`) REFERENCES `dataset` (`dataset_id`) ON DELETE CASCADE,
+  CONSTRAINT `genome_dataset_genome_id_21d55a50_fk_genome_genome_id` FOREIGN KEY (`genome_id`) REFERENCES `genome` (`genome_id`) ON DELETE CASCADE,
+  CONSTRAINT `genome_dataset_release_id_1903f87c_fk_ensembl_release_release_id` FOREIGN KEY (`release_id`) REFERENCES `ensembl_release` (`release_id`) ON DELETE SET NULL
+) ENGINE=InnoDB AUTO_INCREMENT=207766 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `genome_dataset`
+--
+-- WHERE:  genome_id in (86, 5255)
+
+LOCK TABLES `genome_dataset` WRITE;
+/*!40000 ALTER TABLE `genome_dataset` DISABLE KEYS */;
+INSERT INTO `genome_dataset` VALUES (171,1,171,86,1),(172,1,172,86,1),(2459,0,2518,86,1),(61283,0,61336,86,1),(63930,1,63983,86,2),(71737,0,71789,86,NULL),(71738,0,71790,86,NULL),(71739,0,71791,86,NULL),(71740,0,71792,86,NULL),(71741,0,71793,86,NULL),(71742,0,71794,86,NULL),(71743,0,71795,86,NULL),(71744,0,71796,86,NULL),(71745,0,71797,86,NULL),(71746,0,71798,86,NULL),(71747,0,71799,86,NULL),(71748,0,71800,86,NULL),(116153,1,116189,86,3),(116154,1,116190,86,3),(127649,1,127671,86,6),(127650,1,127672,86,6),(127651,1,127673,86,6),(189206,1,127671,86,8),(189207,1,127672,86,8),(189208,1,127673,86,8),(122625,1,171,5255,6),(122626,1,122649,5255,6),(122627,1,122650,5255,6),(122628,1,122651,5255,6),(122629,1,122652,5255,6),(122630,1,122653,5255,6),(122631,1,122654,5255,6),(122632,1,122655,5255,6),(122633,1,122656,5255,6),(122634,1,122657,5255,6),(122635,1,122658,5255,6),(122636,1,122659,5255,6),(122637,1,122660,5255,6),(122638,1,122661,5255,6),(122639,1,122662,5255,6),(122640,1,122663,5255,6),(127668,1,127690,5255,6),(127669,1,127691,5255,6),(195143,1,129601,5255,7),(195144,1,129602,5255,7);
+/*!40000 ALTER TABLE `genome_dataset` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `genome_release`
+--
+
+DROP TABLE IF EXISTS `genome_release`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `genome_release` (
+  `genome_release_id` int(11) NOT NULL AUTO_INCREMENT,
+  `is_current` tinyint(1) NOT NULL,
+  `genome_id` int(11) NOT NULL,
+  `release_id` int(11) NOT NULL,
+  PRIMARY KEY (`genome_release_id`),
+  UNIQUE KEY `unique_genome_release` (`genome_id`,`release_id`),
+  KEY `genome_release_genome_id_3e45dc04_fk_genome_genome_id` (`genome_id`),
+  KEY `genome_release_release_id_bca7e1e5_fk_ensembl_release_release_id` (`release_id`),
+  CONSTRAINT `genome_release_genome_id_3e45dc04_fk_genome_genome_id` FOREIGN KEY (`genome_id`) REFERENCES `genome` (`genome_id`),
+  CONSTRAINT `genome_release_release_id_bca7e1e5_fk_ensembl_release_release_id` FOREIGN KEY (`release_id`) REFERENCES `ensembl_release` (`release_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=8482 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `genome_release`
+--
+-- WHERE:  genome_id in (86, 5255);
+
+LOCK TABLES `genome_release` WRITE;
+/*!40000 ALTER TABLE `genome_release` DISABLE KEYS */;
+INSERT INTO `genome_release` VALUES (111,0,86,1),(7563,0,86,8),(3153,1,5255,6);
+/*!40000 ALTER TABLE `genome_release` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `organism`
+--
+
+DROP TABLE IF EXISTS `organism`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `organism` (
+  `organism_id` int(11) NOT NULL AUTO_INCREMENT,
+  `taxonomy_id` int(11) NOT NULL,
+  `species_taxonomy_id` int(11) DEFAULT NULL,
+  `common_name` varchar(128) DEFAULT NULL,
+  `strain` varchar(128) DEFAULT NULL,
+  `scientific_name` varchar(128) DEFAULT NULL,
+  `biosample_id` varchar(128) NOT NULL,
+  `scientific_parlance_name` varchar(255) DEFAULT NULL,
+  `organism_uuid` char(40) NOT NULL,
+  `strain_type` varchar(128) DEFAULT NULL,
+  `rank` int(11) DEFAULT '0',
+  `ensembl_name` varchar(128) DEFAULT NULL,
+  PRIMARY KEY (`organism_id`),
+  UNIQUE KEY `ensembl_name` (`biosample_id`),
+  UNIQUE KEY `organism_uuid` (`organism_uuid`),
+  KEY `idx_organism_taxonomy_id` (`taxonomy_id`),
+  KEY `idx_organism_species_taxonomy_id` (`species_taxonomy_id`)
+) ENGINE=InnoDB AUTO_INCREMENT=3444 DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `organism`
+--
+-- WHERE:  organism_id in (select organism_id from genome where production_name = 'homo_sapiens');
+
+LOCK TABLES `organism` WRITE;
+/*!40000 ALTER TABLE `organism` DISABLE KEYS */;
+INSERT INTO `organism` VALUES (83,9606,9606,'Human',NULL,'Homo sapiens','SAMN12121739','Human','1d336185-affe-4a91-85bb-04ebd73cbb56',NULL,999,'SAMN12121739');
+/*!40000 ALTER TABLE `organism` ENABLE KEYS */;
+UNLOCK TABLES;
+/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
+
+/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
+/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */;
+/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */;
+/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
+/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */;
+/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
+/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/ensembl_repos/VEP_plugins/plugin_config.txt b/src/python/tests/variation_utils/data/ensembl_repos/VEP_plugins/plugin_config.txt
new file mode 100644
index 00000000..985b821b
--- /dev/null
+++ b/src/python/tests/variation_utils/data/ensembl_repos/VEP_plugins/plugin_config.txt
@@ -0,0 +1,1968 @@
+my $VEP_PLUGIN_CONFIG = {
+  "plugins" => [
+
+    ## PATHOGENICITY PREDICTIONS
+    ############################
+
+    # dbNSFP
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/dbNSFP.pm
+    # Requires tabix-indexed data file as first param
+    # Field names are listed below and rendered as a multi-selectable autocomplete text field
+    # Human, GRCh38 only (3.x), for GRCh37 use 2.9.x
+    {
+      "key" => "dbNSFP",
+      "label" => "dbNSFP",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "dbNSFP provides pathogenicity predictions for missense variants from various algorithms. The scores are provided for non-commercial use, for more details, including using the data commercially, please see https://www.dbnsfp.org/",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/dbNSFP.pm",
+      "requires_data" => 1,
+      "requires_install" => 1,
+      "params"  => [
+        #"/path/to/dbNSFP5.2c_grch38.gz",
+        "@*"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+      "form" => [
+        {
+          "name" => "dbNSFP_fields",
+          "label" => "Fields to include",
+          "helptip" => "Fields to fetch from dbNSFP; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
+          "value" => "",
+          'type' => 'dropdown',
+          'multiple' => 1,
+          'style' => 'height:150px',
+          'required' => 1,
+          'notes' => 'Field descriptions in <a rel="external" href="https://download.genos.us/dbnsfp/release/dbNSFP5.2c.readme.txt">dbNSFP README</a>',
+          # "class" => "jquery-multiselect",
+          "values" => [
+              #"chr",
+              #"pos(1-based)",
+              #"ref",
+              #"alt",
+              #"aaref",
+              #"aaalt",
+              #"rs_dbSNP",
+              #"hg19_chr",
+              #"hg19_pos(1-based)",
+              #"hg18_chr",
+              #"hg18_pos(1-based)",
+              "aapos",
+              "genename",
+              "Ensembl_geneid",
+              "Ensembl_transcriptid",
+              "Ensembl_proteinid",
+              "Uniprot_acc",
+              "Uniprot_entry",
+              #"HGVSc_snpEff",
+              #"HGVSp_snpEff",
+              #"HGVSc_VEP",
+              #"HGVSp_VEP",
+              #"APPRIS",
+              #"GENCODE_basic",
+              #"TSL",
+              #"VEP_canonical",
+              #"MANE",
+              #"cds_strand",
+              #"refcodon",
+              #"codonpos",
+              "codon_degeneracy",
+              #"Ancestral_allele",
+              "AltaiNeandertal",
+              "Denisova",
+              "VindijiaNeandertal",
+              "ChagyrskayaNeandertal",
+              "clinvar_id",
+              "clinvar_clnsig",
+              "clinvar_trait",
+              "clinvar_review",
+              "clinvar_hgvs",
+              "clinvar_var_source",
+              "clinvar_MedGen_id",
+              "clinvar_OMIM_id",
+              "clinvar_Orphanet_id",
+              "Interpro_domain",
+              #"SIFT_score",
+              #"SIFT_converted_rankscore",
+              #"SIFT_pred",
+              #"SIFT4G_score",
+              #"SIFT4G_converted_rankscore",
+              #"SIFT4G_pred",
+              "MutationTaster_score",
+              "MutationTaster_rankscore",
+              "MutationTaster_pred",
+              "MutationTaster_model",
+              "MutationTaster_trees_benign",
+              "MutationTaster_trees_deleterious",
+              "MutationAssessor_score",
+              "MutationAssessor_rankscore",
+              "MutationAssessor_pred",
+              "PROVEAN_score",
+              "PROVEAN_converted_rankscore",
+              "PROVEAN_pred",
+              "MetaSVM_score",
+              "MetaSVM_rankscore",
+              "MetaSVM_pred",
+              "MetaLR_score",
+              "MetaLR_rankscore",
+              "MetaLR_pred",
+              "Reliability_index",
+              "MetaRNN_score",
+              "MetaRNN_rankscore",
+              "MetaRNN_pred",
+              "REVEL_score",
+              "REVEL_rankscore",
+              "MutPred2_score",
+              "MutPred2_rankscore",
+              "MutPred2_pred",
+              "MutPred2_top5_mechanisms",
+              "MVP_score",
+              "MVP_rankscore",
+              "gMVP_score",
+              "gMVP_rankscore",
+              "MPC_score",
+              "MPC_rankscore",
+              "PrimateAI_score",
+              "PrimateAI_rankscore",
+              "PrimateAI_pred",
+              "DEOGEN2_score",
+              "DEOGEN2_rankscore",
+              "DEOGEN2_pred",
+              "BayesDel_addAF_score",
+              "BayesDel_addAF_rankscore",
+              "BayesDel_addAF_pred",
+              "BayesDel_noAF_score",
+              "BayesDel_noAF_rankscore",
+              "BayesDel_noAF_pred",
+              "ClinPred_score",
+              "ClinPred_rankscore",
+              "ClinPred_pred",
+              "LIST-S2_score",
+              "LIST-S2_rankscore",
+              "LIST-S2_pred",
+              "VARITY_R_score",
+              "VARITY_R_rankscore",
+              "VARITY_ER_score",
+              "VARITY_ER_rankscore",
+              "VARITY_R_LOO_score",
+              "VARITY_R_LOO_rankscore",
+              "VARITY_ER_LOO_score",
+              "VARITY_ER_LOO_rankscore",
+              "ESM1b_score",
+              "ESM1b_converted_rankscore",
+              "ESM1b_pred",
+              #"AlphaMissense_score",
+              #"AlphaMissense_rankscore",
+              #"AlphaMissense_pred",
+              "PHACTboost_score",
+              "PHACTboost_rankscore",
+              "MutFormer_score",
+              "MutFormer_rankscore",
+              "Aloft_Fraction_transcripts_affected",
+              "Aloft_prob_Tolerant",
+              "Aloft_prob_Recessive",
+              "Aloft_prob_Dominant",
+              "Aloft_pred",
+              "Aloft_Confidence",
+              "DANN_score",
+              "DANN_rankscore",
+              "fathmm-XF_coding_score",
+              "fathmm-XF_coding_rankscore",
+              "fathmm-XF_coding_pred",
+              "Eigen-raw_coding",
+              "Eigen-raw_coding_rankscore",
+              "Eigen-phred_coding",
+              "Eigen-PC-raw_coding",
+              "Eigen-PC-raw_coding_rankscore",
+              "Eigen-PC-phred_coding",
+              "GERP++_NR",
+              "GERP++_RS",
+              "GERP++_RS_rankscore",
+              "GERP_91_mammals",
+              "GERP_91_mammals_rankscore",
+              "phyloP100way_vertebrate",
+              "phyloP100way_vertebrate_rankscore",
+              "phyloP470way_mammalian",
+              "phyloP470way_mammalian_rankscore",
+              "phyloP17way_primate",
+              "phyloP17way_primate_rankscore",
+              "phastCons100way_vertebrate",
+              "phastCons100way_vertebrate_rankscore",
+              "phastCons470way_mammalian",
+              "phastCons470way_mammalian_rankscore",
+              "phastCons17way_primate",
+              "phastCons17way_primate_rankscore",
+              "bStatistic",
+              "bStatistic_converted_rankscore",
+              "1000Gp3_AC",
+              "1000Gp3_AF",
+              "1000Gp3_AFR_AC",
+              "1000Gp3_AFR_AF",
+              "1000Gp3_EUR_AC",
+              "1000Gp3_EUR_AF",
+              "1000Gp3_AMR_AC",
+              "1000Gp3_AMR_AF",
+              "1000Gp3_EAS_AC",
+              "1000Gp3_EAS_AF",
+              "1000Gp3_SAS_AC",
+              "1000Gp3_SAS_AF",
+              "TOPMed_frz8_AC",
+              "TOPMed_frz8_AN",
+              "TOPMed_frz8_AF",
+              "AllofUs_ALL_AC",
+              "AllofUs_ALL_AN",
+              "AllofUs_ALL_AF",
+              "AllofUs_AFR_AC",
+              "AllofUs_AFR_AN",
+              "AllofUs_AFR_AF",
+              "AllofUs_AMR_AC",
+              "AllofUs_AMR_AN",
+              "AllofUs_AMR_AF",
+              "AllofUs_EAS_AC",
+              "AllofUs_EAS_AN",
+              "AllofUs_EAS_AF",
+              "AllofUs_EUR_AC",
+              "AllofUs_EUR_AN",
+              "AllofUs_EUR_AF",
+              "AllofUs_MID_AC",
+              "AllofUs_MID_AN",
+              "AllofUs_MID_AF",
+              "AllofUs_SAS_AC",
+              "AllofUs_SAS_AN",
+              "AllofUs_SAS_AF",
+              "AllofUs_OTH_AC",
+              "AllofUs_OTH_AN",
+              "AllofUs_OTH_AF",
+              "AllofUs_POPMAX_AF",
+              "AllofUs_POPMAX_AC",
+              "AllofUs_POPMAX_AN",
+              "AllofUs_POPMAX_POP",
+              "gnomAD2.1.1_exomes_flag",
+              "gnomAD2.1.1_exomes_controls_AC",
+              "gnomAD2.1.1_exomes_controls_AN",
+              "gnomAD2.1.1_exomes_controls_AF",
+              "gnomAD2.1.1_exomes_controls_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_AC",
+              "gnomAD2.1.1_exomes_non_neuro_AN",
+              "gnomAD2.1.1_exomes_non_neuro_AF",
+              "gnomAD2.1.1_exomes_non_neuro_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_AC",
+              "gnomAD2.1.1_exomes_non_cancer_AN",
+              "gnomAD2.1.1_exomes_non_cancer_AF",
+              "gnomAD2.1.1_exomes_non_cancer_nhomalt",
+              "gnomAD2.1.1_exomes_controls_AFR_AC",
+              "gnomAD2.1.1_exomes_controls_AFR_AN",
+              "gnomAD2.1.1_exomes_controls_AFR_AF",
+              "gnomAD2.1.1_exomes_controls_AFR_nhomalt",
+              "gnomAD2.1.1_exomes_controls_AMR_AC",
+              "gnomAD2.1.1_exomes_controls_AMR_AN",
+              "gnomAD2.1.1_exomes_controls_AMR_AF",
+              "gnomAD2.1.1_exomes_controls_AMR_nhomalt",
+              "gnomAD2.1.1_exomes_controls_ASJ_AC",
+              "gnomAD2.1.1_exomes_controls_ASJ_AN",
+              "gnomAD2.1.1_exomes_controls_ASJ_AF",
+              "gnomAD2.1.1_exomes_controls_ASJ_nhomalt",
+              "gnomAD2.1.1_exomes_controls_EAS_AC",
+              "gnomAD2.1.1_exomes_controls_EAS_AN",
+              "gnomAD2.1.1_exomes_controls_EAS_AF",
+              "gnomAD2.1.1_exomes_controls_EAS_nhomalt",
+              "gnomAD2.1.1_exomes_controls_FIN_AC",
+              "gnomAD2.1.1_exomes_controls_FIN_AN",
+              "gnomAD2.1.1_exomes_controls_FIN_AF",
+              "gnomAD2.1.1_exomes_controls_FIN_nhomalt",
+              "gnomAD2.1.1_exomes_controls_NFE_AC",
+              "gnomAD2.1.1_exomes_controls_NFE_AN",
+              "gnomAD2.1.1_exomes_controls_NFE_AF",
+              "gnomAD2.1.1_exomes_controls_NFE_nhomalt",
+              "gnomAD2.1.1_exomes_controls_SAS_AC",
+              "gnomAD2.1.1_exomes_controls_SAS_AN",
+              "gnomAD2.1.1_exomes_controls_SAS_AF",
+              "gnomAD2.1.1_exomes_controls_SAS_nhomalt",
+              "gnomAD2.1.1_exomes_controls_POPMAX_AC",
+              "gnomAD2.1.1_exomes_controls_POPMAX_AN",
+              "gnomAD2.1.1_exomes_controls_POPMAX_AF",
+              "gnomAD2.1.1_exomes_controls_POPMAX_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_AFR_AC",
+              "gnomAD2.1.1_exomes_non_neuro_AFR_AN",
+              "gnomAD2.1.1_exomes_non_neuro_AFR_AF",
+              "gnomAD2.1.1_exomes_non_neuro_AFR_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_AMR_AC",
+              "gnomAD2.1.1_exomes_non_neuro_AMR_AN",
+              "gnomAD2.1.1_exomes_non_neuro_AMR_AF",
+              "gnomAD2.1.1_exomes_non_neuro_AMR_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_ASJ_AC",
+              "gnomAD2.1.1_exomes_non_neuro_ASJ_AN",
+              "gnomAD2.1.1_exomes_non_neuro_ASJ_AF",
+              "gnomAD2.1.1_exomes_non_neuro_ASJ_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_EAS_AC",
+              "gnomAD2.1.1_exomes_non_neuro_EAS_AN",
+              "gnomAD2.1.1_exomes_non_neuro_EAS_AF",
+              "gnomAD2.1.1_exomes_non_neuro_EAS_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_FIN_AC",
+              "gnomAD2.1.1_exomes_non_neuro_FIN_AN",
+              "gnomAD2.1.1_exomes_non_neuro_FIN_AF",
+              "gnomAD2.1.1_exomes_non_neuro_FIN_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_NFE_AC",
+              "gnomAD2.1.1_exomes_non_neuro_NFE_AN",
+              "gnomAD2.1.1_exomes_non_neuro_NFE_AF",
+              "gnomAD2.1.1_exomes_non_neuro_NFE_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_SAS_AC",
+              "gnomAD2.1.1_exomes_non_neuro_SAS_AN",
+              "gnomAD2.1.1_exomes_non_neuro_SAS_AF",
+              "gnomAD2.1.1_exomes_non_neuro_SAS_nhomalt",
+              "gnomAD2.1.1_exomes_non_neuro_POPMAX_AC",
+              "gnomAD2.1.1_exomes_non_neuro_POPMAX_AN",
+              "gnomAD2.1.1_exomes_non_neuro_POPMAX_AF",
+              "gnomAD2.1.1_exomes_non_neuro_POPMAX_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_AFR_AC",
+              "gnomAD2.1.1_exomes_non_cancer_AFR_AN",
+              "gnomAD2.1.1_exomes_non_cancer_AFR_AF",
+              "gnomAD2.1.1_exomes_non_cancer_AFR_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_AMR_AC",
+              "gnomAD2.1.1_exomes_non_cancer_AMR_AN",
+              "gnomAD2.1.1_exomes_non_cancer_AMR_AF",
+              "gnomAD2.1.1_exomes_non_cancer_AMR_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_ASJ_AC",
+              "gnomAD2.1.1_exomes_non_cancer_ASJ_AN",
+              "gnomAD2.1.1_exomes_non_cancer_ASJ_AF",
+              "gnomAD2.1.1_exomes_non_cancer_ASJ_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_EAS_AC",
+              "gnomAD2.1.1_exomes_non_cancer_EAS_AN",
+              "gnomAD2.1.1_exomes_non_cancer_EAS_AF",
+              "gnomAD2.1.1_exomes_non_cancer_EAS_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_FIN_AC",
+              "gnomAD2.1.1_exomes_non_cancer_FIN_AN",
+              "gnomAD2.1.1_exomes_non_cancer_FIN_AF",
+              "gnomAD2.1.1_exomes_non_cancer_FIN_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_NFE_AC",
+              "gnomAD2.1.1_exomes_non_cancer_NFE_AN",
+              "gnomAD2.1.1_exomes_non_cancer_NFE_AF",
+              "gnomAD2.1.1_exomes_non_cancer_NFE_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_SAS_AC",
+              "gnomAD2.1.1_exomes_non_cancer_SAS_AN",
+              "gnomAD2.1.1_exomes_non_cancer_SAS_AF",
+              "gnomAD2.1.1_exomes_non_cancer_SAS_nhomalt",
+              "gnomAD2.1.1_exomes_non_cancer_POPMAX_AC",
+              "gnomAD2.1.1_exomes_non_cancer_POPMAX_AN",
+              "gnomAD2.1.1_exomes_non_cancer_POPMAX_AF",
+              "gnomAD2.1.1_exomes_non_cancer_POPMAX_nhomalt",
+              "gnomAD4.1_joint_flag",
+              "gnomAD4.1_joint_AC",
+              "gnomAD4.1_joint_AN",
+              "gnomAD4.1_joint_AF",
+              "gnomAD4.1_joint_nhomalt",
+              "gnomAD4.1_joint_POPMAX_AC",
+              "gnomAD4.1_joint_POPMAX_AN",
+              "gnomAD4.1_joint_POPMAX_AF",
+              "gnomAD4.1_joint_POPMAX_nhomalt",
+              "gnomAD4.1_joint_AFR_AC",
+              "gnomAD4.1_joint_AFR_AN",
+              "gnomAD4.1_joint_AFR_AF",
+              "gnomAD4.1_joint_AFR_nhomalt",
+              "gnomAD4.1_joint_AMI_AC",
+              "gnomAD4.1_joint_AMI_AN",
+              "gnomAD4.1_joint_AMI_AF",
+              "gnomAD4.1_joint_AMI_nhomalt",
+              "gnomAD4.1_joint_AMR_AC",
+              "gnomAD4.1_joint_AMR_AN",
+              "gnomAD4.1_joint_AMR_AF",
+              "gnomAD4.1_joint_AMR_nhomalt",
+              "gnomAD4.1_joint_ASJ_AC",
+              "gnomAD4.1_joint_ASJ_AN",
+              "gnomAD4.1_joint_ASJ_AF",
+              "gnomAD4.1_joint_ASJ_nhomalt",
+              "gnomAD4.1_joint_EAS_AC",
+              "gnomAD4.1_joint_EAS_AN",
+              "gnomAD4.1_joint_EAS_AF",
+              "gnomAD4.1_joint_EAS_nhomalt",
+              "gnomAD4.1_joint_FIN_AC",
+              "gnomAD4.1_joint_FIN_AN",
+              "gnomAD4.1_joint_FIN_AF",
+              "gnomAD4.1_joint_FIN_nhomalt",
+              "gnomAD4.1_joint_MID_AC",
+              "gnomAD4.1_joint_MID_AN",
+              "gnomAD4.1_joint_MID_AF",
+              "gnomAD4.1_joint_MID_nhomalt",
+              "gnomAD4.1_joint_NFE_AC",
+              "gnomAD4.1_joint_NFE_AN",
+              "gnomAD4.1_joint_NFE_AF",
+              "gnomAD4.1_joint_NFE_nhomalt",
+              "gnomAD4.1_joint_SAS_AC",
+              "gnomAD4.1_joint_SAS_AN",
+              "gnomAD4.1_joint_SAS_AF",
+              "gnomAD4.1_joint_SAS_nhomalt",
+              "ALFA_European_AC",
+              "ALFA_European_AN",
+              "ALFA_European_AF",
+              "ALFA_African_Others_AC",
+              "ALFA_African_Others_AN",
+              "ALFA_African_Others_AF",
+              "ALFA_East_Asian_AC",
+              "ALFA_East_Asian_AN",
+              "ALFA_East_Asian_AF",
+              "ALFA_African_American_AC",
+              "ALFA_African_American_AN",
+              "ALFA_African_American_AF",
+              "ALFA_Latin_American_1_AC",
+              "ALFA_Latin_American_1_AN",
+              "ALFA_Latin_American_1_AF",
+              "ALFA_Latin_American_2_AC",
+              "ALFA_Latin_American_2_AN",
+              "ALFA_Latin_American_2_AF",
+              "ALFA_Other_Asian_AC",
+              "ALFA_Other_Asian_AN",
+              "ALFA_Other_Asian_AF",
+              "ALFA_South_Asian_AC",
+              "ALFA_South_Asian_AN",
+              "ALFA_South_Asian_AF",
+              "ALFA_Other_AC",
+              "ALFA_Other_AN",
+              "ALFA_Other_AF",
+              "ALFA_African_AC",
+              "ALFA_African_AN",
+              "ALFA_African_AF",
+              "ALFA_Asian_AC",
+              "ALFA_Asian_AN",
+              "ALFA_Asian_AF",
+              "ALFA_Total_AC",
+              "ALFA_Total_AN",
+              "ALFA_Total_AF",
+              "dbNSFP_POPMAX_AF",
+              "dbNSFP_POPMAX_AC",
+              "dbNSFP_POPMAX_POP",
+              #"Gene_name",
+              #"Ensembl_gene",
+              #"chr",
+              #"Gene_old_names",
+              #"Gene_other_names",
+              #"Uniprot_acc(HGNC/Uniprot)",
+              #"Uniprot_id(HGNC/Uniprot)",
+              #"Entrez_gene_id",
+              #"CCDS_id",
+              #"Refseq_id",
+              #"ucsc_id",
+              #"MIM_id",
+              #"OMIM_id",
+              #"Gene_full_name",
+              "Pathway(Uniprot)",
+              "Pathway(BioCarta)_short",
+              "Pathway(BioCarta)_full",
+              "Pathway(ConsensusPathDB)",
+              "Pathway(KEGG)_id",
+              "Pathway(KEGG)_full",
+              "Function_description",
+              "Disease_description",
+              "MIM_phenotype_id",
+              "MIM_disease",
+              "Orphanet_disorder_id",
+              "Orphanet_disorder",
+              "Orphanet_association_type",
+              "GenCC_id",
+              "GenCC_disease_title",
+              "GenCC_impact_class",
+              "GenCC_model_of_inheritance",
+              "GenCC_pmid",
+              "Trait_association(GWAS)",
+              "MGI_mouse_gene",
+              "MGI_mouse_phenotype",
+              "ZFIN_zebrafish_gene",
+              "ZFIN_zebrafish_structure",
+              "ZFIN_zebrafish_phenotype_quality",
+              "ZFIN_zebrafish_phenotype_tag",
+              "HPO_id",
+              "HPO_name",
+              "GO_biological_process",
+              "GO_cellular_component",
+              "GO_molecular_function",
+              "P(HI)",
+              "HIPred_score",
+              "HIPred",
+              "GHIS",
+              "ClinGen_Haploinsufficiency_Score",
+              "ClinGen_Haploinsufficiency_Description",
+              "ClinGen_Haploinsufficiency_PMID",
+              "ClinGen_Haploinsufficiency_Disease",
+              "P(rec)",
+              "Known_rec_info",
+              "RVIS_EVS",
+              "RVIS_percentile_EVS",
+              "LoF-FDR_ExAC",
+              "RVIS_ExAC",
+              "RVIS_percentile_ExAC",
+              "ExAC_pLI",
+              "ExAC_pRec",
+              "ExAC_pNull",
+              "ExAC_nonTCGA_pLI",
+              "ExAC_nonTCGA_pRec",
+              "ExAC_nonTCGA_pNull",
+              "ExAC_nonpsych_pLI",
+              "ExAC_nonpsych_pRec",
+              "ExAC_nonpsych_pNull",
+              "gnomAD_pLI",
+              "gnomAD_pRec",
+              "gnomAD_pNull",
+              "ExAC_del.score",
+              "ExAC_dup.score",
+              "ExAC_cnv.score",
+              "ExAC_cnv_flag",
+              "GDI",
+              "GDI-Phred",
+              "Gene damage prediction (all disease-causing genes)",
+              "Gene damage prediction (all Mendelian disease-causing genes)",
+              "Gene damage prediction (Mendelian AD disease-causing genes)",
+              "Gene damage prediction (Mendelian AR disease-causing genes)",
+              "Gene damage prediction (all PID disease-causing genes)",
+              "Gene damage prediction (PID AD disease-causing genes)",
+              "Gene damage prediction (PID AR disease-causing genes)",
+              "Gene damage prediction (all cancer disease-causing genes)",
+              "Gene damage prediction (cancer recessive disease-causing genes)",
+              "Gene damage prediction (cancer dominant disease-causing genes)",
+              "LoFtool_score",
+              "Essential_gene",
+              "Essential_gene_CRISPR",
+              "Essential_gene_CRISPR2",
+              "Essential_gene_gene-trap",
+              "Gene_indispensability_score",
+              "Gene_indispensability_pred",
+              "Tissue_specificity(Uniprot)",
+              "HPA_consensus_adipose_tissue",
+              "HPA_consensus_adrenal_gland",
+              "HPA_consensus_amygdala",
+              "HPA_consensus_appendix",
+              "HPA_consensus_basal_ganglia",
+              "HPA_consensus_bone_marrow",
+              "HPA_consensus_breast",
+              "HPA_consensus_cerebellum",
+              "HPA_consensus_cerebral_cortex",
+              "HPA_consensus_cervix",
+              "HPA_consensus_choroid_plexus",
+              "HPA_consensus_colon",
+              "HPA_consensus_duodenum",
+              "HPA_consensus_endometrium",
+              "HPA_consensus_epididymis",
+              "HPA_consensus_esophagus",
+              "HPA_consensus_fallopian_tube",
+              "HPA_consensus_gallbladder",
+              "HPA_consensus_heart_muscle",
+              "HPA_consensus_hippocampal_formation",
+              "HPA_consensus_hypothalamus",
+              "HPA_consensus_kidney",
+              "HPA_consensus_liver",
+              "HPA_consensus_lung",
+              "HPA_consensus_lymph_node",
+              "HPA_consensus_midbrain",
+              "HPA_consensus_ovary",
+              "HPA_consensus_pancreas",
+              "HPA_consensus_parathyroid_gland",
+              "HPA_consensus_pituitary_gland",
+              "HPA_consensus_placenta",
+              "HPA_consensus_prostate",
+              "HPA_consensus_rectum",
+              "HPA_consensus_retina",
+              "HPA_consensus_salivary_gland",
+              "HPA_consensus_seminal_vesicle",
+              "HPA_consensus_skeletal_muscle",
+              "HPA_consensus_skin",
+              "HPA_consensus_small_intestine",
+              "HPA_consensus_smooth_muscle",
+              "HPA_consensus_spinal_cord",
+              "HPA_consensus_spleen",
+              "HPA_consensus_stomach",
+              "HPA_consensus_testis",
+              "HPA_consensus_thymus",
+              "HPA_consensus_thyroid_gland",
+              "HPA_consensus_tongue",
+              "HPA_consensus_tonsil",
+              "HPA_consensus_urinary_bladder",
+              "HPA_consensus_vagina",
+              "HPA_consensus_highly_expressed",
+          ],
+        },
+        {
+          "name" => "dbNSFP_transcript_match",
+          "label" => "Transcript match",
+          "helptip" => "By default, some dbNSFP fields contain values for all Ensembl transcripts. Select this to only return values for the matched Ensembl transcript.",
+          "value" => "transcript_match=1",
+          "type" => "checkbox",
+          "style" => "height:150px"
+        }
+      ]
+    },
+
+    # AlphaMissense
+    {
+      "key" => "AlphaMissense",
+      "label" => "AlphaMissense",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/AlphaMissense.pm",
+      "helptip" => "Annotates missense variants with the pre-computed AlphaMissense pathogenicity scores. AlphaMissense is a deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants.",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"file=/path/to/AlphaMissense_hg38.tsv.gz"
+      ]
+    },
+
+    # AVADA
+    {
+      "key" => "AVADA",
+      "label" => "AVADA",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/AVADA.pm",
+    },
+
+    # CADD
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/CADD.pm
+    {
+      "key" => "CADD",
+      "label" => "CADD",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "Combined Annotation Dependent Depletion (CADD) is a tool for scoring the deleteriousness of single nucleotide variants and insertion/deletion variants in the human genome. CADD integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations. CADD is only available here for non-commercial use. See CADD website for more information.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/CADD.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens",
+        "sus_scrofa"
+      ],
+      "form" => [
+        {
+          "name" => "file_type",
+          "label" => "Select annotation file",
+          "type" => "dropdown",
+          "helptip" => "Select type of CADD annotation file to be used. Caution to be taken while using snv, indels or snv_indels options with structural variants as input. It can match unnecessary huge amount of lines in annotation file and in such cases no CADD annotation will be made.",
+          "values" => [
+            { "value" => "snv_indels", "caption" => "CADD SNVs and InDels annotation file", "class" => "_stt_Homo_sapiens" },
+            { "value" => "snv", "caption" => "CADD SNVs annotation file" },
+            { "value" => "indels", "caption" => "CADD InDels annotation file", "class" => "_stt_Homo_sapiens" },
+            { "value" => "sv", "caption" => "CADD-SV annotation file (supported only in GRCh38)", "class" => "_stt_Homo_sapiens" }
+          ],
+          "value" => "snv_indels",
+        },
+      ],
+      "params" => [
+        #"snv=/path/to/CADD_whole_genome_SNVs.tsv.gz",
+        #"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
+        #"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
+        #"sv=/path/to/CADD_prescored_variants.tsv.gz"
+      ]
+    },
+
+    # CAPICE
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/CAPICE.pm
+    # Requires tabix-indexed data files as params (one for InDels, another for SNVs)
+    # No other parameters so no form required
+    # data file currently only available for GRCh37
+    {
+      "key" => "CAPICE",
+      "label" => "CAPICE",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations (CAPICE) is a tool for scoring the pathogenicity of single nucleotide variants and insertion/deletion variants in the human genome. CAPICE uses a gradient boosting tree model trained with multiple genomic annotations used by CADD score and based on clinical significance.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/CAPICE.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/capice_v1.0_build37_indels.tsv.gz",
+        #"/path/to/capice_v1.0_build37_snvs.tsv.gz"
+      ]
+    },
+
+    # FATHMM
+    {
+      "key" => "FATHMM",
+      "label" => "FATHMM",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/FATHMM.pm"
+    },
+
+    # FATHMM-MKL
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/FATHMM_MKL.pm
+    # Requires tabix-indexed data file as first param
+    # No other parameters so no form required
+    # data file currently only available for GRCh37
+    {
+      "key" => "FATHMM_MKL",
+      "label" => "FATHMM-MKL",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "FATHMM-MKL predicts functional consequences of variants, both coding and non-coding.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/FATHMM_MKL.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/fathmm-MKL_Current.tab.gz"
+      ]
+    },
+
+    # GWAVA
+    # https://www.sanger.ac.uk/sanger/StatGen_Gwava
+    # Requires tabix-indexed BED data file from ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/
+    # data file currently only available for GRCh37
+    {
+      "key" => "Gwava",
+      "label" => "GWAVA",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "Retrieves precomputed Genome Wide Annotation of VAriants (GWAVA) scores for any  variant that overlaps a known variant from the Ensembl variation database",
+      "plugin_url" => "ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/VEP_plugin/Gwava.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        "@*",
+        # "/path/to/gwava_scores.bed.gz"
+      ],
+      "form" => [
+        {
+          "name" => "model",
+          "label" => "Model",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "region",    "caption" => "Region" },
+            { "value" => "tss",       "caption" => "TSS" },
+            { "value" => "unmatched", "caption" => "Unmatched" }
+          ],
+          "value" => "region",
+        },
+      ],
+    },
+
+    # Carol
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/Carol.pm
+    # Requires Math/CDF Perl module
+    {
+      "key" => "Carol",
+      "helptip" => "Calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Carol.pm",
+      "requires_install" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    # Condel
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/Condel.pm
+    # Requires path to config directory as first param
+    # config directory is checked out as part of VEP_plugins repo, as /[path]/VEP_plugins/config/Condel/config
+    # Within that dir, edit condel_SP.conf so that condel.dir points to /[path]/VEP_plugins/config/Condel
+    {
+      "key" => "Condel",
+      "helptip" => "Calculates the Consensus Deleteriousness (Condel) score for a missense mutation based on the pre-calculated SIFT and PolyPhen scores",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Condel.pm",
+      "requires_install" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/config/Condel/config",
+        "@*"
+      ],
+      "form" => [
+        {
+          "name" => "score_pred",
+          "label" => "Score/prediction",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "b", "caption" => "Prediction and score" },
+            { "value" => "p", "caption" => "Prediction only" },
+            { "value" => "s", "caption" => "Score only" }
+          ],
+          "value" => "b",
+        },
+      ],
+    },
+
+    # LOFTEE
+    # See https://github.com/konradjk/loftee for details
+    {
+      "key" => "LoF",
+      "helptip" => "LOFTEE identifies LoF (loss-of-function) variation",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm",
+      "requires_data" => 1,
+      "requires_install" => 1,
+      "params" => [
+        "@*"
+      ]
+    },
+
+    # LoFtool
+    # Requires LoFtool_scores.txt file as first param (available in VEP_plugins GitHub repo)
+    {
+      "key" => "LoFtool",
+      "helptip" => "Provides a per-gene rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations in ExAC data",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/LoFtool.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/LoFtool_scores.txt"
+      ]
+    },
+
+    # MPC
+    # Requires fordist_constraint_official_mpc_values.txt.gz data file
+    {
+      "key" => "MPC",
+      "helptip" => "MPC is a missense deleteriousness metric based on the analysis of genic regions depleted of missense mutations in ExAC",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/MPC.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/fordist_constraint_official_mpc_values.txt.gz"
+      ]
+    },
+
+    # MTR
+    # Requires mtrflatfile_1.0.txt.gz data file from ftp://mtr-viewer.mdhs.unimelb.edu.au/pub
+    {
+      "key" => "MTR",
+      "helptip" => "MTR scores quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/MTR.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/mtrflatfile_1.0.txt.gz"
+      ]
+    },
+
+    # PrimateAI
+    # Requires PrimateAI_scores_v0.2.tsv.gz or PrimateAI_scores_v0.2_hg38.tsv.gz from https://basespace.illumina.com/s/yYGFdGih1rXL.
+    {
+      "key" => "PrimateAI",
+      "helptip" => "PrimateAI scores can be used to assess pathogenicity of variants in humans",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/PrimateAI.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/PrimateAI_scores_v0.2_GRCh38_sorted.tsv.bgz
+      ]
+    },
+
+    # REVEL
+    # Requires data file processed from revel_all_chromosomes.csv.zip
+    {
+      "key" => "REVEL",
+      "helptip" => "An ensemble method for predicting the pathogenicity of rare missense variants",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/REVEL.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/revel_all_chromosomes.tsv.gz"
+      ]
+    },
+
+    # PON_P2
+    {
+      "key" => "PON_P2",
+      "label" => "PON_P2",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/PON_P2.pm"
+    },
+
+    # ClinPred
+    # Requires data file processed from ClinPred.txt.gz
+    {
+      "key" => "ClinPred",
+      "helptip" => "A prediction tool for the identification of disease-relevant nonsynonymous single nucleotide variants",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/ClinPred.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/ClinPred_tabbed.tsv.gz"
+      ]
+    },
+
+    # EVE
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/EVE.pm
+    # Requires tabix-indexed data file as params
+    # No other parameters so no form required
+    # data file currently only available for GRCh38
+    # We only report EVE scores for input variants and
+    # don't consider adjacent variants.
+    {
+      "key" => "EVE",
+      "label" => "EVE",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "EVE (evolutionary model of variant effect) is a computational method for the classification of human genetic variants trained solely on evolutionary sequences.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/EVE.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/eve_merged.vcf.gz"
+      ]
+    },
+
+    # Paralogues
+    {
+      "key" => "Paralogues",
+      "label" => "Paralogue variants",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Variant data",
+      "helptip" => "Retrieves ClinVar variants that overlap genomic coordinates corresponding to aligned amino acid positions in paralogous proteins",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Paralogues.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"matches=/path/to/paralogues_matches.tsv.gz",
+        "@*"
+      ],
+      "form" => [
+        {
+          "name" => "clnsig",
+          "label" => "Clinical significance",
+          "helptip" => "Clinical significance term used to filter paralogue variants",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "clnsig=pathogenic",             "caption" => "Pathogenic" },
+            { "value" => "clnsig=benign",                 "caption" => "Benign" },
+            { "value" => "clnsig=uncertain_significance", "caption" => "Uncertain significance" },
+            { "value" => "clnsig=ignore",                 "caption" => "Ignore (fetch all paralogue variants)" }
+          ],
+          "value" => "clnsig=pathogenic"
+        },
+        {
+          "name" => "clnsig_match",
+          "label" => "Clinical significance match type",
+          "helptip" => "Type of match when filtering paralogue variants based on clinical significance (e.g., using 'Pathogenic' and 'Partial match' will fetch variants that are pathogenic and likely pathogenic, whereas 'Exact match' will only fetch pathogenic variants)",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "clnsig_match=partial", "caption" => "Partial match" },
+            { "value" => "clnsig_match=exact",   "caption" => "Exact match" }
+          ],
+          "value" => "clnsig_match=partial"
+        }
+      ]
+    },
+
+    # BayesDel
+    {
+      "key" => "BayesDel",
+      "label" => "BayesDel",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "BayesDel adds a deleteriousness meta-score combining multiple deleteriousness predictors.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/BayesDel.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/BayesDel.vcf.gz"
+      ]
+    },
+
+    # PolyPhen_SIFT
+    {
+      "key" => "PolyPhen_SIFT",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/PolyPhen_SIFT.pm",
+    },
+
+    ## SPLICING PREDICTIONS
+    #######################
+
+    # dbscSNV
+    {
+      "key" => "dbscSNV",
+      "label" => "dbscSNV",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "helptip" => "Retrieves data for splicing variants from a tabix-indexed dbscSNV file",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/dbscSNV.pm",
+      "requires_data" => 1,
+      "requires_install" => 1,
+      "params"  => [
+        #"/path/to/dbscSNV1.1.txt.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    # GeneSplicer
+    {
+      "key" => "GeneSplicer",
+      "label" => "GeneSplicer",
+      "helptip" => "Detects splice sites in genomic DNA",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/GeneSplicer.pm",
+      "requires_install" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/genesplicer/bin/linux/genesplicer",
+        #"/path/to/genesplicer/human",
+        "@*"
+      ]
+    },
+
+    # MaxEntScan
+    {
+      "key" => "MaxEntScan",
+      "label" => "MaxEntScan",
+      "helptip" => "Sequence motif and maximum entropy based splice site consensus predictions",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/MaxEntScan.pm",
+      "requires_install" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"/path/to/maxentscan"
+      ]
+    },
+
+    # SpliceRegion
+    {
+      "key" => "SpliceRegion",
+      "label" => "SpliceRegion",
+      "helptip" => "More granular predictions of splicing effects",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SpliceRegion.pm",
+    },
+
+    # SpliceAI
+    {
+      "key" => "SpliceAI",
+      "label" => "SpliceAI",
+      "helptip" => "Pre-calculated annotations from SpliceAI a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence. Used for non-commercial purposes (https://github.com/Illumina/SpliceAI)",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SpliceAI.pm",
+      "species" => [
+        "homo_sapiens"
+      ],
+      "form" => [
+        {
+          "name" => "file_type",
+          "label" => "Select analysis mode",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "snv", "caption" => "Masked scores (Ensembl/GENCODE v24 canonical transcripts)" },
+            { "value" => "snv_ensembl", "caption" => "Raw scores (Ensembl/GENCODE v37 MANE transcripts, SNV only)" }
+          ],
+          "value" => "snv",
+        },
+      ],
+    },
+
+    # SpliceVault
+    {
+      "key" => "SpliceVault",
+      "label" => "SpliceVault",
+      "helptip" => "Retrieves the most common variant-associated mis-splicing events for variants that overlap a near-splice-site region",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Splicing predictions",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SpliceVault.pm",
+    },
+
+
+    ## CONSERVATION
+    ###############
+
+    # Blosum62
+    {
+      "key" => "Blosum62",
+      "label" => "BLOSUM62",
+      "helptip" => "BLOSUM62 amino acid conservation score",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Conservation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Blosum62.pm",
+    },
+
+    # Conservation
+    # Use the following query to get valid species sets:
+    #
+    # SELECT group_concat(concat("_stt_", gd.name) SEPARATOR ' '), REPLACE(mlss.name, "Gerp Conservation Scores ", ""), sst.value
+    #   FROM method_link ml,
+    #     method_link_species_set mlss,
+    #     genome_db gd, species_set ss, species_set_tag sst
+    #   WHERE mlss.method_link_id = ml.method_link_id AND
+    #     mlss.species_set_id = ss.species_set_id AND
+    #     ss.genome_db_id = gd.genome_db_id AND
+    #     ss.species_set_id = sst.species_set_id AND
+    #     (ml.class = "ConservationScore.conservation_score")
+    #   GROUP BY mlss.species_set_id
+    {
+      "key" => "Conservation",
+      "helptip" => "Retrieves a conservation score from the Ensembl Compara databases for variant positions",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Conservation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Conservation.pm",
+      "params" => [
+        "@*"
+      ],
+      "form" => [
+        {
+          "name" => "method_link_type",
+          "label" => "Method",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "GERP_CONSERVATION_SCORE", "caption" => "GERP"}
+          ]
+        },
+        {
+          "name" => "species_set",
+          "label" => "Species set",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "mammals",    "caption" => "39 eutherian mammals"   }, #"class" => "_stt_macaca_mulatta _stt_echinops_telfairi _stt_tupaia_belangeri _stt_erinaceus_europaeus _stt_sorex_araneus _stt_microcebus_murinus _stt_pongo_abelii _stt_equus_caballus _stt_ochotona_princeps _stt_cavia_porcellus _stt_choloepus_hoffmanni _stt_procavia_capensis _stt_tursiops_truncatus _stt_tarsius_syrichta _stt_dipodomys_ordii _stt_vicugna_pacos _stt_pteropus_vampyrus _stt_loxodonta_africana _stt_oryctolagus_cuniculus _stt_ailuropoda_melanoleuca _stt_nomascus_leucogenys _stt_callithrix_jacchus _stt_myotis_lucifugus _stt_bos_taurus _stt_gorilla_gorilla _stt_otolemur_garnettii _stt_pan_troglodytes _stt_ictidomys_tridecemlineatus _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_mustela_putorius_furo _stt_felis_catus _stt_ovis_aries _stt_dasypus_novemcinctus _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
+            { "value" => "amniotes",   "caption" => "23 amniota vertebrates" }, #"class" => "_stt_macaca_mulatta _stt_ornithorhynchus_anatinus _stt_monodelphis_domestica _stt_pongo_abelii _stt_equus_caballus _stt_taeniopygia_guttata _stt_oryctolagus_cuniculus _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_callithrix_jacchus _stt_bos_taurus _stt_gorilla_gorilla _stt_pan_troglodytes _stt_sus_scrofa _stt_mus_musculus _stt_canis_familiaris _stt_felis_catus _stt_gallus_gallus _stt_ovis_aries _stt_homo_sapiens _stt_papio_anubis _stt_chlorocebus_sabaeus _stt_rattus_norvegicus" },
+            { "value" => "sauropsids", "caption" => "7 sauropsids"           }, #"class" => "_stt_taeniopygia_guttata _stt_anolis_carolinensis _stt_meleagris_gallopavo _stt_pelodiscus_sinensis _stt_gallus_gallus _stt_anas_platyrhynchos _stt_ficedula_albicollis" },
+            { "value" => "fish",       "caption" => "11 fish"                }, #"class" => "_stt_takifugu_rubripes _stt_gasterosteus_aculeatus _stt_oryzias_latipes _stt_tetraodon_nigroviridis _stt_gadus_morhua _stt_oreochromis_niloticus _stt_xiphophorus_maculatus _stt_astyanax_mexicanus _stt_lepisosteus_oculatus _stt_poecilia_formosa _stt_danio_rerio" },
+          ]
+        },
+      ]
+    },
+
+    # AncestralAllele
+    # Requires processed FASTA file from https://ftp.ensembl.org/pub/current_fasta/ancestral_alleles/
+    {
+      "key" => "AncestralAllele",
+      "label" => "Ancestral allele",
+      "helptip" => "Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Conservation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/AncestralAllele.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/homo_sapiens_ancestor_GRCh38_e93.fa.gz"
+      ]
+    },
+
+
+
+    ## FREQUENCY DATA
+    #################
+
+    # gnomADc
+    {
+      "key" => "gnomADc",
+      "label" => "gnomADc",
+      "helptip" => "Reports coverage data from the gmomAD coverage files",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Frequency data",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/gnomADc.pm",
+      "requires_data" => 1,
+       "species" => [
+        "homo_sapiens"
+      ]
+    },
+
+
+
+    ## PHENOTYPES DATA AND CITATIONS
+    ##################
+
+    # Phenotypes
+    {
+      "key" => "Phenotypes",
+      "label" => "Phenotypes",
+      "helptip" => "Retrieves overlapping phenotype annotations",
+      "section" => "Phenotype data and citations",
+      "requires_data" => 1,
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Phenotypes.pm",
+      "params" => [
+        #"/path/to/Phenotypes_data_files/phenotypes_dir_with_dumps_for_all_species.gvf.gz"
+      ]
+    },
+
+    # GO
+    {
+      "key" => "GO",
+      "label" => "Gene Ontology",
+      "helptip" => "Retrieves Gene Ontology terms associated with transcripts/translations",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/GO.pm",
+      "section" => "Phenotype data and citations",
+      "params" => [
+        #"/path/to/GO_data_dir"
+      ]
+    },
+
+    # G2P
+    {
+      "key" => "G2P",
+      "label" => "G2P",
+      "helptip" => "Assesses variants using G2P allelic requirements for potential phenotype involvement.",
+      "available" => 0,
+      "enabled" => 0,
+      "requires_data" => 1,
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/G2P.pm",
+    },
+
+    # Geno2MP
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/Geno2MP.pm
+    # Requires tabix-indexed VCF data file
+    {
+      "key" => "Geno2MP",
+      "label" => "Geno2MP",
+      "helptip" => "Geno2MP is a web-accessible database of rare variant genotypes linked to individual-level phenotypic profiles defined by human phenotype ontology (HPO) terms",
+      "available" => 0,
+      "enabled" => 0,
+      "requires_data" => 1,
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Geno2MP.pm",
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        "#file=/path/to/Geno2MP/data.vcf.gz"
+      ],
+    },
+
+    # PostGAP
+    {
+      "key" => "PostGAP",
+      "label" => "PostGAP",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/PostGAP.pm"
+    },
+
+    # satMutMPRA
+    {
+      "key" => "satMutMPRA",
+      "helptip" => "Reports saturation mutagenesis MPRA measures of variant effects on gene RNA expression for 21 enhancers/promoters",
+      "section" => "Phenotype data and citations",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/satMutMPRA.pm",
+    },
+
+    # Mastermind
+    {
+      "key" => "Mastermind",
+      "label" => "Mastermind",
+      "helptip" => "Variants with clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (https://www.genomenon.com/mastermind)",
+      "available" => 0,
+      "enabled" => 0,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Mastermind.pm"
+    },
+
+    # GWAS
+    {
+      "key" => "GWAS",
+      "label" => "GWAS",
+      "helptip" => "Genome-wide associated study data from the NHGRI-EBI GWAS Catalog (https://www.ebi.ac.uk/gwas/)",
+      "available" => 0,
+      "enabled" => 0,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/GWAS.pm"
+    },
+
+    # PhenotypeOrthologous
+    {
+      "key" => "PhenotypeOrthologous",
+      "label" => "PhenotypeOrthologous",
+      "helptip" => "Phenotypes associated with orthologous genes in model organisms (mouse and rat)",
+      "requires_data" => 1,
+      "available" => 0,
+      "enabled" => 0,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "section" => "Phenotype data and citations",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/PhenotypeOrthologous.pm"
+    },
+
+
+
+    ## VARIANT DATA
+    ###############
+
+    # DeNovo
+    {
+      "key" => "DeNovo",
+      "helptip" => "Identifies de novo variants in a VCF file",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Variant data",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/DeNovo.pm",
+    },
+
+    # Open Targets Genetics
+    {
+      "key" => "OpenTargets",
+      "label" => "Open Targets Genetics",
+      "helptip" => "Returns locus-to-gene (L2G) scores to predict causal genes at GWAS loci from Open Targets Genetics",
+      "enabled" => 0,
+      "available" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/OpenTargets.pm",
+      "section" => "Variant data",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        #"file=/path/to/OpenTargets_data.tsv.gz"
+      ]
+    },
+
+    # LD
+    {
+      "key" => "LD",
+      "label" => "Linkage disequilibrium",
+      "helptip" => "Finds variants in linkage disequilibrium with any overlapping existing variants from the Ensembl variation databases",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/LD.pm",
+      "section" => "Variant data",
+      "params" => [
+        "@*"
+      ],
+      "form" => [
+        {
+          "name" => "population",
+          "label" => "Population",
+          "type" => "dropdown",
+          "values" => [
+            { "value" => "1000GENOMES:phase_3:ACB", "caption" => "African Caribbean in Barbados" },
+            { "value" => "1000GENOMES:phase_3:ASW", "caption" => "African Ancestry in Southwest US" },
+            { "value" => "1000GENOMES:phase_3:BEB", "caption" => "Bengali in Bangladesh" },
+            { "value" => "1000GENOMES:phase_3:CDX", "caption" => "Chinese Dai in Xishuangbanna, China" },
+            { "value" => "1000GENOMES:phase_3:CEU", "caption" => "Utah residents with Northern and Western European ancestry" },
+            { "value" => "1000GENOMES:phase_3:CHB", "caption" => "Han Chinese in Bejing, China" },
+            { "value" => "1000GENOMES:phase_3:CHS", "caption" => "Southern Han Chinese, China" },
+            { "value" => "1000GENOMES:phase_3:CLM", "caption" => "Colombian in Medellin, Colombia" },
+            { "value" => "1000GENOMES:phase_3:ESN", "caption" => "Esan in Nigeria" },
+            { "value" => "1000GENOMES:phase_3:FIN", "caption" => "Finnish in Finland" },
+            { "value" => "1000GENOMES:phase_3:GBR", "caption" => "British in England and Scotland" },
+            { "value" => "1000GENOMES:phase_3:GIH", "caption" => "Gujarati Indian in Houston, TX" },
+            { "value" => "1000GENOMES:phase_3:IBS", "caption" => "Iberian populations in Spain" },
+            { "value" => "1000GENOMES:phase_3:ITU", "caption" => "Indian Telugu in the UK" },
+            { "value" => "1000GENOMES:phase_3:JPT", "caption" => "Japanese in Tokyo, Japan" },
+            { "value" => "1000GENOMES:phase_3:KHV", "caption" => "Kinh in Ho Chi Minh City, Vietnam" },
+            { "value" => "1000GENOMES:phase_3:LWK", "caption" => "Luhya in Webuye, Kenya" },
+            { "value" => "1000GENOMES:phase_3:MAG", "caption" => "Mandinka in The Gambia" },
+            { "value" => "1000GENOMES:phase_3:MSL", "caption" => "Mende in Sierra Leone" },
+            { "value" => "1000GENOMES:phase_3:MXL", "caption" => "Mexican Ancestry in Los Angeles, California" },
+            { "value" => "1000GENOMES:phase_3:PEL", "caption" => "Peruvian in Lima, Peru" },
+            { "value" => "1000GENOMES:phase_3:PJL", "caption" => "Punjabi in Lahore, Pakistan" },
+            { "value" => "1000GENOMES:phase_3:PUR", "caption" => "Puerto Rican in Puerto Rico" },
+            { "value" => "1000GENOMES:phase_3:STU", "caption" => "Sri Lankan Tamil in the UK" },
+            { "value" => "1000GENOMES:phase_3:TSI", "caption" => "Toscani in Italy" },
+            { "value" => "1000GENOMES:phase_3:YRI", "caption" => "Yoruba in Ibadan, Nigeria" },
+          ],
+          "value" => "1000GENOMES:phase_3:CEU",
+        },
+        {
+          "name" => "threshold",
+          "label" => "r2 cutoff",
+          "type" => "string",
+          "value" => 0.8,
+        },
+      ]
+    },
+
+    # SameCodon
+    {
+      "key" => "SameCodon",
+      "label" => "Variants in same codon",
+      "helptip" => "Reports existing variants that fall in the same codon",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SameCodon.pm",
+      "section" => "Variant data",
+    },
+
+    # LOVD
+    {
+      "key" => "LOVD",
+      "label" => "LOVD",
+      "helptip" => "Retrieves LOVD variation data",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/LOVD.pm",
+      "section" => "Variant data",
+    },
+
+    # SubsetVCF
+    {
+      "key" => "SubsetVCF",
+      "label" => "SubsetVCF",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Variant data",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SubsetVCF.pm"
+    },
+    # GeneBe
+    {
+      "key" => "GeneBe",
+      "label" => "GeneBe",
+      "helptip" => "Retrieves automatic ACMG variant classification data from GeneBe",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Variant data",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/GeneBe.pm",
+    },
+
+
+    ## NEARBY FEATURES
+    ##################
+
+    # NearestGene
+    {
+      "key" => "NearestGene",
+      "label" => "Nearest gene",
+      "helptip" => "Finds the nearest gene to non-genic variants",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Nearby features",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/NearestGene.pm",
+    },
+
+    # NearestExonJB
+    {
+      "key" => "NearestExonJB",
+      "label" => "NearestExonJB",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Nearby features",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/NearestExonJB.pm"
+    },
+
+    # Downstream
+    {
+      "key" => "Downstream",
+      "label" => "Downstream",
+      "helptip" => "Predicts the downstream effects of a frameshift variant on the protein sequence of a transcript",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Nearby features",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Downstream.pm",
+    },
+
+    # TSSDistance
+    {
+      "key" => "TSSDistance",
+      "label" => "TSS distance",
+      "helptip" => "Calculates the distance from the transcription start site for upstream variants   ",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Nearby features",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/TSSDistance.pm",
+    },
+
+
+
+    ## SEQUENCE
+    ###########
+
+    # ProteinSeqs
+    {
+      "key" => "ProteinSeqs",
+      "label" => "Protein sequences",
+      "helptip" => "Prints out the reference and mutated protein sequences of any proteins found with non-synonymous mutations",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Sequence",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/ProteinSeqs.pm",
+    },
+
+    # ReferenceQuality
+    {
+      "key" => "ReferenceQuality",
+      "label" => "ReferenceQuality",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Sequence",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/ReferenceQuality.pm"
+    },
+
+
+
+    ## VISUALISATION
+    ################
+
+    # Draw
+    {
+      "key" => "Draw",
+      "label" => "Draw",
+      "helptip" => "Creates images of the transcript model showing variant location",
+      "available" => 0,
+      "enabled" => 0,
+      "requires_install" => 1,
+      "section" => "Visualisation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Draw.pm",
+    },
+
+
+
+    ## LOCAL ID
+    ###########
+
+    # LocalID
+    {
+      "key" => "LocalID",
+      "label" => "LocalID",
+      "helptip" => "Allows you to use variant IDs as VEP input without making a database connection.",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Look up",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/LocalID.pm",
+    },
+
+
+
+    ## EXTERNAL ID
+    ##############
+
+    # FlagLRG
+    {
+      "key" => "FlagLRG",
+      "label" => "FlagLRG",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "External ID",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/FlagLRG.pm"
+    },
+
+
+
+    ## MOTIF
+    ########
+
+    # FunMotifs
+    {
+      "key" => "FunMotifs",
+      "label" => "FunMotifs",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Motif",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/FunMotifs.pm"
+    },
+
+
+
+    ## HGVS
+    #######
+
+    # HGVSIntronOffset
+    {
+      "key" => "HGVSIntronOffset",
+      "label" => "HGVSIntronOffset",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "HGVS",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/HGVSIntronOffset.pm"
+    },
+
+    # SingleLetterAA
+    {
+      "key" => "SingleLetterAA",
+      "label" => "SingleLetterAA",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "HGVS",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/SingleLetterAA.pm"
+    },
+
+
+
+    ## STRUCTURAL VARIANT DATA
+    ##########################
+
+    # StructuralVariantOverlap
+    {
+      "key" => "StructuralVariantOverlap",
+      "label" => "StructuralVariantOverlap",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Structural variant data",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/StructuralVariantOverlap.pm"
+    },
+
+    ## GENE TOLERANCE TO CHANGE
+    ###########################
+
+    # DosageSensitivity
+    {
+      "key" => "DosageSensitivity",
+      "label" => "DosageSensitivity",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Gene tolerance to change",
+      "helptip" => "DosageSensitivity determines the likelihood of a gene being haploinsufficient or triplosensitive",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/DosageSensitivity.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#file=/path/to/Collins_rCNV_2022.dosage_sensitivity_scores.tsv.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    # LOEUF
+    # Requires data file processed from supplementary_dataset_11_full_constraint_metrics.tsv.gz
+    # Only available for GRCh37
+    {
+      "key" => "LOEUF",
+      "helptip" => "LOEUF stands for the 'loss-of-function observed/expected upper bound fraction'. This plugin adds constraint scores derived from gnomAD to VEP",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Gene tolerance to change",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/LOEUF.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params"  => [
+        # "/path/to/loeuf_dataset.gz",
+        "@*"
+      ]
+    },
+
+
+    # MechPredict
+    {
+      "key" => "MechPredict",
+      "label" => "MechPredict", 
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Gene tolerance to change",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/MechPredict.pm",
+    },
+
+    # pLI
+    # Requires pLI_values.txt file as first param (available in VEP_plugins GitHub repo)
+    {
+      "key" => "pLI",
+      "helptip" => "Provides a per-gene or per transcript probability of being loss-of-function intolerant (pLI)",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Gene tolerance to change",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/pLI.pm",
+      "requires_data" => 1,
+      "species" => [
+        "homo_sapiens"
+      ],
+      "params" => [
+        # "/path/to/pLI_values.txt"
+      ]
+    },
+
+    ## TRANSCRIPT ANNOTATION
+    ############
+
+    # NMD
+    {
+      "key" => "NMD",
+      "helptip" => "Nonsense-mediated mRNA decay escaping variants prediction",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Transcript annotation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/NMD.pm"
+    },
+
+    # UTRAnnotator
+    # https://github.com/ensembl-variation/VEP_plugins/blob/main/UTRAnnotator.pm
+    {
+      "key" => "UTRAnnotator",
+      "label" => "UTRAnnotator",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Transcript annotation",
+      "helptip" => "A VEP plugin that annotates the effect of 5' UTR variant especially for variant creating/disrupting upstream ORFs.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/UTRAnnotator.pm"
+    },
+
+    # TranscriptAnnotator
+    {
+      "key" => "TranscriptAnnotator",
+      "label" => "TranscriptAnnotator",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Transcript annotation",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/TranscriptAnnotator.pm"
+    },
+
+    # RiboseqORFs
+    {
+      "key" => "RiboseqORFs",
+      "label" => "RiboseqORFs",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Transcript annotation",
+      "helptip" => "A VEP plugin that calculates consequences for variants overlapping Ribo-seq ORFs",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/RiboseqORFs.pm",
+      "params"  => [
+        #"file=/path/to/Ribo-seq_ORFs.bed.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    ## PROTEIN DATA
+    ###############
+
+    # neXtProt
+    {
+      "key" => "neXtProt",
+      "label" => "neXtProt",
+      "helptip" => "Retrieves protein-related data from neXtProt",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Protein data",
+      "requires_data" => 1,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/neXtProt.pm"
+    },
+
+    ## PROTEIN ANNOTATION
+    #####################
+
+    # IntAct
+    {
+      "key" => "IntAct",
+      "label" => "IntAct",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Functional effect",
+      "helptip" => "IntAct provides molecular interaction data for variants as reported by IntAct database",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/IntAct.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#mapping_file=/path/to/mutation_gc_map.txt.gz",
+        "#mutation_file=/path/to/mutations.tsv",
+        "@*"
+      ],
+      "species" => [
+        "homo_sapiens",
+        "mus_musculus",
+        "rattus_norvegicus",
+        "gallus_gallus_gca000002315v5",
+        "saccharomyces_cerevisiae",
+        "arabidopsis_thaliana",
+        "drosophila_melanogaster"
+      ],
+      "form" => [
+        {
+          "name" => "IntAct_efields",
+          "label" => "Extra fields to include",
+          "helptip" => "Extra fields to show; hold down the Ctrl (Windows) / Command (Mac) button to select multiple options",
+          "value" => "",
+          "type" => "dropdown",
+          "multiple" => 1,
+          "style" => "height:150px",
+          "values" => [
+            { "value" => "feature_ac=1", "caption" => "Feature AC" },
+            { "value" => "feature_short_label=1", "caption" => "Feature short label" },
+            { "value" => "feature_annotation=1", "caption" => "Feature annotation" },
+            { "value" => "ap_ac=1", "caption" => "Affected protein AC" },
+            { "value" => "interaction_participants=1", "caption" => "Interaction participants" },
+            { "value" => "pmid=1", "caption" => "PubMedID" },
+          ],
+        },
+      ]
+    },
+
+    # MaveDB
+    {
+      "key" => "MaveDB",
+      "label" => "MaveDB",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Functional effect",
+      "helptip" => "MaveDB holds experimentally determined measures of variant effect",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/MaveDB.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#file=/path/to/MaveDB_variants.tsv.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    # VARITY
+    {
+      "key" => "VARITY",
+      "label" => "VARITY",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Pathogenicity predictions",
+      "helptip" => "VARITY is a tool to predict pathogenicity of rare human missense variants. VARITY uses a gradient boosting tree model trained with rare variants from multiple genomic annotations and based on clinical significance.",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/VARITY.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#file=/path/to/varity_all_predictions.tsv.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+    # mutfunc
+    {
+      "key" => "mutfunc",
+      "label" => "mutfunc",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Protein annotation",
+      "helptip" => "mutfunc predicts destabilization effect of protein structure, interaction, regulatory region etc. caused by a variant",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/mutfunc.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#db=/path/to/mutfunc_data.db",
+        "@*"
+      ],
+      "species" => [
+        "homo_sapiens",
+        "saccharomyces_cerevisiae"
+      ],
+      "form" => [
+        {
+          "name" => "mutfunc_fields",
+          "label" => "Fields to include",
+          "helptip" => "Select which analysis you want to see in the output",
+          "value" => "",
+          "type" => "checklist",
+          "multiple" => 1,
+          "style" => "height:150px",
+          "values" => [
+            { "value" => "motif=1", "caption" => "Linear Motifs", "helptip" => "Effect on linear motifs", 'checked' => 1 },
+            { "value" => "int=1", "caption" => "Protein Interactions", "helptip" => "Effect on protein interactions", 'checked' => 1 },
+            { "value" => "mod=1", "caption" => "Protein Structure", "helptip" => "Effect on protein structure", 'checked' => 1 },
+            { "value" => "exp=1", "caption" => "Protein Structure (exp.)", "helptip" => "Effect on protein structure (experimental)", 'checked' => 1 }
+          ],
+        }
+      ]
+    },
+
+    ## REGULATORY IMPACT
+    ####################
+
+    # Enformer
+    {
+      "key" => "Enformer",
+      "label" => "Enformer",
+      "available" => 0,
+      "enabled" => 0,
+      "section" => "Regulatory impact",
+      "helptip" => "Predictions of variant impact on gene expression",
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/Enformer.pm",
+      "requires_data" => 1,
+      "params"  => [
+        "#file=/path/to/enformer_variants.vcf.gz"
+      ],
+      "species" => [
+        "homo_sapiens"
+      ],
+    },
+
+
+    ## OTHER
+    ########
+
+    # CSN
+    {
+      "key" => "CSN",
+      "helptip" => "Reports Clinical Sequencing Nomenclature (CSN) for variants",
+      "available" => 0,
+      "enabled" => 0,
+      "plugin_url" => "https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/115/CSN.pm",
+    },
+  ]
+};
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz b/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz
new file mode 100644
index 00000000..44d64382
--- /dev/null
+++ b/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz
@@ -0,0 +1,5 @@
+##CADD GRCh38-v1.7 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health at Charite - Universitatsmedizin Berlin 2013-2023. All rights reserved.
+#Chrom  Pos     Ref     Alt     RawScore        PHRED
+1       10061   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC        0.530575        5.774
+1       10067   T       TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC      0.524375        5.712
+1       10108   C       CA      0.459250        5.036
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz b/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz
new file mode 100644
index 00000000..505d51c8
--- /dev/null
+++ b/src/python/tests/variation_utils/data/enseweb-data_tools/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz
@@ -0,0 +1,5 @@
+##CADD GRCh38-v1.7 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health at Charite - Universitatsmedizin Berlin 2013-2023. All rights reserved.
+#Chrom  Pos     Ref     Alt     RawScore        PHRED
+1       10001   T       A       0.767991        7.993
+1       10001   T       C       0.799933        8.285
+1       10001   T       G       0.777613        8.080
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump b/src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump
new file mode 100644
index 00000000..f54abe26
--- /dev/null
+++ b/src/python/tests/variation_utils/data/homo_sapiens_core_110_38.dump
@@ -0,0 +1,151 @@
+-- MySQL dump 10.13  Distrib 5.7.44, for Linux (x86_64)
+--
+-- Host: mysql-ens-sta-6    Database: homo_sapiens_core_110_38
+-- ------------------------------------------------------
+-- Server version	5.7.27-30-log
+
+/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
+/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
+/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
+/*!40101 SET NAMES utf8 */;
+/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
+/*!40103 SET TIME_ZONE='+00:00' */;
+/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
+/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
+/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
+/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
+
+--
+-- Table structure for table `meta`
+--
+
+DROP TABLE IF EXISTS `meta`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `meta` (
+  `meta_id` int(11) NOT NULL AUTO_INCREMENT,
+  `species_id` int(10) unsigned DEFAULT '1',
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+) ENGINE=MyISAM AUTO_INCREMENT=6625 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+/*!40101 SET character_set_client = @saved_cs_client */;
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+--
+-- Dumping data for table `meta`
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+LOCK TABLES `meta` WRITE;
+/*!40000 ALTER TABLE `meta` DISABLE KEYS */;
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+/*!40000 ALTER TABLE `seq_region` ENABLE KEYS */;
+UNLOCK TABLES;
+
+
+--
+-- Table structure for table `seq_region_synonym`
+--
+
+DROP TABLE IF EXISTS `seq_region_synonym`;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!40101 SET character_set_client = utf8 */;
+CREATE TABLE `seq_region_synonym` (
+  `seq_region_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `seq_region_id` int(10) unsigned NOT NULL,
+  `synonym` varchar(250) NOT NULL,
+  `external_db_id` int(10) unsigned DEFAULT NULL,
+  PRIMARY KEY (`seq_region_synonym_id`),
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=4717 DEFAULT CHARSET=latin1 ROW_FORMAT=DYNAMIC;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `seq_region_synonym`
+--
+
+LOCK TABLES `seq_region_synonym` WRITE;
+/*!40000 ALTER TABLE `seq_region_synonym` DISABLE KEYS */;
+INSERT INTO `seq_region_synonym` VALUES 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69,2006448172,'chr5_MU273353v1_fix',11000),(4670,2006448174,'chr5_MU273356v1_alt',11000),(4671,2006448176,'chr5_MU273355v1_fix',11000),(4672,2006448178,'chr5_MU273352v1_fix',11000),(4673,2006448180,'chr6_MU273357v1_alt',11000),(4674,2006448182,'chr7_MU273358v1_alt',11000),(4675,2006448184,'chr8_MU273362v1_fix',11000),(4676,2006448186,'chr8_MU273359v1_fix',11000),(4677,2006448188,'chr8_MU273361v1_fix',11000),(4678,2006448190,'chr8_MU273363v1_fix',11000),(4679,2006448192,'chr8_MU273360v1_fix',11000),(4680,2006448194,'chr9_MU273366v1_fix',11000),(4681,2006448196,'chr9_MU273364v1_fix',11000),(4682,2006448198,'chr9_MU273365v1_fix',11000),(4683,2006448200,'chr10_MU273367v1_fix',11000),(4684,2006448202,'chr11_KQ759759v2_fix',11000),(4685,2006448204,'chr11_MU273369v1_fix',11000),(4686,2006448206,'chr11_MU273371v1_fix',11000),(4687,2006448208,'chr11_MU273370v1_fix',11000),(4688,2006448210,'chr11_MU273368v1_alt',11000),(4689,2006448212,'chr12_MU273372v1_fix',11000),(4690,2006448214,'chr14_MU273373v1_fix',11000),(4691,2006448216,'chr15_MU273375v1_alt',11000),(4692,2006448218,'chr15_MU273374v1_fix',11000),(4693,2006448220,'chr16_MU273376v1_fix',11000),(4694,2006448222,'chr16_MU273377v1_fix',11000),(4695,2006448224,'chr17_MU273380v1_fix',11000),(4696,2006448226,'chr17_MU273378v1_alt',11000),(4697,2006448228,'chr17_MU273383v1_fix',11000),(4698,2006448230,'chr17_MU273379v1_fix',11000),(4699,2006448232,'chr17_MU273382v1_fix',11000),(4700,2006448234,'chr17_MU273381v1_fix',11000),(4701,2006448236,'chr19_MU273387v1_alt',11000),(4702,2006448238,'chr19_MU273384v1_fix',11000),(4703,2006448240,'chr19_MU273385v1_fix',11000),(4704,2006448242,'chr20_MU273388v1_fix',11000),(4705,2006448244,'chr20_MU273389v1_fix',11000),(4706,2006448246,'chr21_MU273390v1_fix',11000),(4707,2006448248,'chr21_MU273391v1_fix',11000),(4708,2006448250,'chr21_MU273392v1_fix',11000),(4709,2006448252,'chr22_KQ759762v2_fix',11000),(4710,2006448254,'chrX_MU273397v1_alt',11000),(4711,2006448256,'chrX_MU273393v1_fix',11000),(4712,2006448258,'chrX_MU273394v1_fix',11000),(4713,2006448260,'chrX_MU273396v1_alt',11000),(4714,2006448262,'chrX_MU273395v1_alt',11000),(4715,2006448264,'chrY_MU273398v1_fix',11000),(4716,131216,'na',1830);
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+UNLOCK TABLES;
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+/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
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diff --git a/src/python/tests/variation_utils/data/test.vcf.bgz b/src/python/tests/variation_utils/data/test.vcf.bgz
new file mode 100644
index 00000000..53880a09
Binary files /dev/null and b/src/python/tests/variation_utils/data/test.vcf.bgz differ
diff --git a/src/python/tests/variation_utils/data/test.vcf.gz b/src/python/tests/variation_utils/data/test.vcf.gz
new file mode 100644
index 00000000..56b09d02
Binary files /dev/null and b/src/python/tests/variation_utils/data/test.vcf.gz differ
diff --git a/src/python/tests/variation_utils/file_locator/test_fasta.py b/src/python/tests/variation_utils/file_locator/test_fasta.py
new file mode 100644
index 00000000..009d0d7c
--- /dev/null
+++ b/src/python/tests/variation_utils/file_locator/test_fasta.py
@@ -0,0 +1,60 @@
+import pytest
+
+from ensembl.variation_utils.clients import core, metadata
+from ensembl.variation_utils.file_locator import fasta, ftp
+
+class TestFASTALocatorFactory():
+    @pytest.fixture
+    def fasta_locator_factory(self):
+        return fasta.FASTALocatorFactory()
+
+    def test_default(self, fasta_locator_factory):
+        assert fasta_locator_factory._locator is None
+        
+    def test_set_locator(self, fasta_locator_factory):
+        fasta_locator_factory.set_locator("current")
+        assert type(fasta_locator_factory._locator) is fasta.FTPFASTALocator
+
+        fasta_locator_factory.set_locator("old")
+        assert type(fasta_locator_factory._locator) is fasta.OldFTPFASTALocator
+
+        with pytest.raises(Exception):
+            fasta_locator_factory.set_locator("non_existing")
+
+class TestFTPFASTALocator():
+    @pytest.fixture()
+    def ftp_fasta_locator(self):
+        return fasta.FTPFASTALocator()
+    
+    @pytest.fixture()
+    def metadata_client(self, ini_file):
+        return metadata.MetadataDBClient(ini_file=ini_file)
+
+    def test_defaults(self, ftp_fasta_locator):
+        # default storage media - disk
+        assert ftp_fasta_locator._storage_media == ftp.StorageMediaType.DISK
+        assert ftp_fasta_locator.base_path == "/path/to/ftp/dir"
+
+    def test_locate_file(self, ftp_fasta_locator, metadata_client):
+        ftp_fasta_locator.metadata_client = metadata_client
+        assert ftp_fasta_locator.locate_file("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "/path/to/ftp/dir/Homo_sapiens/GCA_000001405.29/genome/unmasked.fa.gz"
+
+class TestOldFTPFASTALocator():
+    @pytest.fixture()
+    def old_ftp_fasta_locator(self):
+        return fasta.OldFTPFASTALocator()
+    
+    @pytest.fixture()
+    def core_db_client(self, ini_file):
+        return core.CoreDBClient(ini_file=ini_file, species="homo_sapiens", version="110")
+
+    def test_defaults(self, old_ftp_fasta_locator):
+        assert old_ftp_fasta_locator._storage_media == ftp.StorageMediaType.DISK
+        assert old_ftp_fasta_locator._division == "EnsemblVertebrates" 
+        assert old_ftp_fasta_locator._assembly == "GRCh38"
+
+        assert old_ftp_fasta_locator.base_path == "/path/to/old/ftp/dir"
+
+    def test_locate_file(self, old_ftp_fasta_locator, core_db_client):
+        old_ftp_fasta_locator.core_db_client = core_db_client
+        assert old_ftp_fasta_locator.locate_file() == "/path/to/old/ftp/dir/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz"
diff --git a/src/python/tests/variation_utils/file_locator/test_file_locator.py b/src/python/tests/variation_utils/file_locator/test_file_locator.py
new file mode 100644
index 00000000..fa2f4498
--- /dev/null
+++ b/src/python/tests/variation_utils/file_locator/test_file_locator.py
@@ -0,0 +1,14 @@
+import pytest
+
+from ensembl.variation_utils.file_locator import file_locator
+
+class TestAbstractClass():
+    def test_file_locator(self):
+        with pytest.raises(TypeError) as excinfo:
+            file_locator.FileLocator()
+        assert "Can't instantiate abstract class FileLocator" in str(excinfo.value)
+
+    def test_file_locator_factory(self):
+        with pytest.raises(TypeError) as excinfo:
+            file_locator.FileLocatorFactory()
+        assert "Can't instantiate abstract class FileLocatorFactory" in str(excinfo.value)
diff --git a/src/python/tests/variation_utils/file_locator/test_ftp.py b/src/python/tests/variation_utils/file_locator/test_ftp.py
new file mode 100644
index 00000000..85d96866
--- /dev/null
+++ b/src/python/tests/variation_utils/file_locator/test_ftp.py
@@ -0,0 +1,94 @@
+import pytest
+
+from ensembl.variation_utils.clients import core, metadata
+from ensembl.variation_utils.file_locator import ftp
+
+class TestFTPFileLocator():
+    @pytest.fixture
+    def metadata_db_client(self, ini_file):
+        return metadata.MetadataDBClient(ini_file=ini_file)
+
+    @pytest.fixture
+    def ftp_file_locator(self):
+        return ftp.FTPFileLocator()
+
+    def test_defaults(self, ftp_file_locator):
+        # default storage media - disk
+        assert ftp_file_locator._storage_media == ftp.StorageMediaType.DISK
+        assert ftp_file_locator.base_path == "/path/to/ftp/dir"
+
+    def test_storage_media_update(self, ftp_file_locator):
+        ftp_file_locator.storage_media = ftp.StorageMediaType.SERVER
+
+        assert ftp_file_locator.storage_media == ftp.StorageMediaType.SERVER
+        assert ftp_file_locator.base_path == "https://ftp.ebi.ac.uk/pub/ensemblorganisms"
+
+    def test_species_name(self, ftp_file_locator, metadata_db_client):
+        ftp_file_locator.metadata_client = metadata_db_client
+
+        assert ftp_file_locator.get_species_name("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "Homo_sapiens"
+        with pytest.raises(Exception):
+            ftp_file_locator.get_species_name("non_existing")
+
+    def test_assembly(self, ftp_file_locator, metadata_db_client):
+        ftp_file_locator.metadata_client = metadata_db_client
+
+        assert ftp_file_locator.get_assembly("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "GCA_000001405.29"
+        with pytest.raises(Exception):
+            ftp_file_locator.get_assembly("non_existing")
+
+class TestOldFTPFileLocator():
+    @pytest.fixture()
+    def core_db_client(self, ini_file):
+        core_db_client = core.CoreDBClient(ini_file=ini_file)
+        core_db_client.update_db(species="homo_sapiens", version="110")
+
+        return core_db_client
+    
+    @pytest.fixture()
+    def old_ftp_file_locator(self):
+        return ftp.OldFTPFileLocator()
+
+    def test_defaults(self, old_ftp_file_locator):
+        # default storage media - disk
+        assert old_ftp_file_locator._storage_media == ftp.StorageMediaType.DISK
+        assert old_ftp_file_locator._division == "EnsemblVertebrates" 
+        assert old_ftp_file_locator._assembly == "GRCh38"
+
+        assert old_ftp_file_locator.base_path == "/path/to/old/ftp/dir"
+
+    def test_change_storage_media(self, old_ftp_file_locator):
+        old_ftp_file_locator.storage_media = ftp.StorageMediaType.SERVER
+
+        assert old_ftp_file_locator.storage_media == ftp.StorageMediaType.SERVER
+        assert old_ftp_file_locator.base_path == "https://ftp.ensembl.org/pub"
+
+    def test_change_division(self, old_ftp_file_locator):
+        old_ftp_file_locator.division = "EnsemblPlants"
+        assert old_ftp_file_locator.base_path == "/path/to/old/ftp/dir"
+
+        old_ftp_file_locator.storage_media = ftp.StorageMediaType.SERVER
+        assert old_ftp_file_locator.base_path == "https://ftp.ensemblgenomes.org/pub"
+
+    def test_change_assembly(self, old_ftp_file_locator):
+        old_ftp_file_locator.assembly = "GRCh37"
+        assert old_ftp_file_locator.base_path == "/path/to/old/ftp/dir"
+
+        old_ftp_file_locator.storage_media = ftp.StorageMediaType.SERVER
+        assert old_ftp_file_locator.base_path == "https://ftp.ensembl.org/pub/grch37"
+
+    def test_division_segment(self, old_ftp_file_locator):
+        assert old_ftp_file_locator.get_division_segment() == ""
+
+        old_ftp_file_locator.division = "EnsemblPlants"
+        assert old_ftp_file_locator.get_division_segment() == "plants"
+
+        old_ftp_file_locator.division = "EnsemblMetazoa"
+        assert old_ftp_file_locator.get_division_segment() == "metazoa"
+
+    def test_version(self, old_ftp_file_locator, core_db_client):
+        with pytest.raises(Exception):
+            old_ftp_file_locator.get_version()
+
+        old_ftp_file_locator.core_db_client = core_db_client
+        old_ftp_file_locator.get_version() == "110"
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/file_locator/test_gff.py b/src/python/tests/variation_utils/file_locator/test_gff.py
new file mode 100644
index 00000000..cd131460
--- /dev/null
+++ b/src/python/tests/variation_utils/file_locator/test_gff.py
@@ -0,0 +1,37 @@
+import pytest
+
+from ensembl.variation_utils.clients import metadata
+from ensembl.variation_utils.file_locator import gff, ftp
+
+class TestGFFLocatorFactory():
+    @pytest.fixture
+    def gff_locator_factory(self):
+        return gff.GFFLocatorFactory()
+
+    def test_default(self, gff_locator_factory):
+        assert gff_locator_factory._locator is None
+        
+    def test_set_locator(self, gff_locator_factory):
+        gff_locator_factory.set_locator("current")
+        assert type(gff_locator_factory._locator) is gff.FTPGFFLocator
+
+        with pytest.raises(Exception):
+            gff_locator_factory.set_locator("old")
+
+class TestFTPGFFLocator():
+    @pytest.fixture()
+    def ftp_gff_locator(self):
+        return gff.FTPGFFLocator()
+    
+    @pytest.fixture()
+    def metadata_client(self, ini_file):
+        return metadata.MetadataDBClient(ini_file=ini_file)
+
+    def test_defaults(self, ftp_gff_locator):
+        # default storage media - disk
+        assert ftp_gff_locator._storage_media == ftp.StorageMediaType.DISK
+        assert ftp_gff_locator.base_path == "/path/to/ftp/dir"
+
+    def test_locate_file(self, ftp_gff_locator, metadata_client):
+        ftp_gff_locator.metadata_client = metadata_client
+        assert ftp_gff_locator.locate_file("2b5fb047-5992-4dfb-b2fa-1fb4e18d1abb") == "/path/to/ftp/dir/Homo_sapiens/GCA_000001405.29/ensembl/geneset/2024_11/genes.gff3.gz"
diff --git a/src/python/tests/variation_utils/file_locator/test_vep_cache.py b/src/python/tests/variation_utils/file_locator/test_vep_cache.py
new file mode 100644
index 00000000..e4b8439c
--- /dev/null
+++ b/src/python/tests/variation_utils/file_locator/test_vep_cache.py
@@ -0,0 +1,39 @@
+import pytest
+
+from ensembl.variation_utils.clients import core
+from ensembl.variation_utils.file_locator import ftp, vep_cache
+
+class TestVEPCacheLocatorFactory():
+    @pytest.fixture
+    def vep_cache_locator_factory(self):
+        return vep_cache.VEPCacheLocatorFactory()
+
+    def test_default(self, vep_cache_locator_factory):
+        assert vep_cache_locator_factory._locator is None
+        
+    def test_set_locator(self, vep_cache_locator_factory):
+        vep_cache_locator_factory.set_locator("old")
+        assert type(vep_cache_locator_factory._locator) is vep_cache.OldFTPVEPCahceLocator
+
+        with pytest.raises(Exception):
+            vep_cache_locator_factory.set_locator("non_existing")
+
+class TestOldFTPVEPCahceLocator():
+    @pytest.fixture()
+    def old_vep_cache_locator(self):
+        return vep_cache.OldFTPVEPCahceLocator()
+    
+    @pytest.fixture()
+    def core_db_client(self, ini_file):
+        return core.CoreDBClient(ini_file=ini_file, species="homo_sapiens", version="110")
+
+    def test_defaults(self, old_vep_cache_locator):
+        assert old_vep_cache_locator._storage_media == ftp.StorageMediaType.DISK
+        assert old_vep_cache_locator._division == "EnsemblVertebrates" 
+        assert old_vep_cache_locator._assembly == "GRCh38"
+
+        assert old_vep_cache_locator.base_path == "/path/to/old/ftp/dir"
+
+    def test_locate_file(self, old_vep_cache_locator, core_db_client):
+        old_vep_cache_locator.core_db_client = core_db_client
+        assert old_vep_cache_locator.locate_file() == "/path/to/old/ftp/dir/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz"
diff --git a/src/python/tests/variation_utils/test_file_utils.py b/src/python/tests/variation_utils/test_file_utils.py
new file mode 100644
index 00000000..d9865cc3
--- /dev/null
+++ b/src/python/tests/variation_utils/test_file_utils.py
@@ -0,0 +1,14 @@
+import os
+
+from ensembl.variation_utils import file_utils
+
+class TestFileUtils():
+    def test_bgzip(self, data_dir):
+        file = os.path.join(data_dir, "test.vcf.bgz")
+
+        assert file_utils.is_bgzip(file)
+
+    def test_not_bgzip(self, data_dir):
+        file = os.path.join(data_dir, "test.vcf.gz")
+
+        assert not file_utils.is_bgzip(file)
\ No newline at end of file
diff --git a/src/python/tests/variation_utils/vep_config/test_plugin.py b/src/python/tests/variation_utils/vep_config/test_plugin.py
new file mode 100644
index 00000000..3f56f562
--- /dev/null
+++ b/src/python/tests/variation_utils/vep_config/test_plugin.py
@@ -0,0 +1,76 @@
+import os
+import pytest
+from unittest import mock
+
+from ensembl.variation_utils.vep_config import plugin
+
+class TestAbstractClass():
+    def test_plugin_args_builder(self):
+        with pytest.raises(TypeError) as excinfo:
+            plugin.PluginArgsBuilder()
+        assert "Can't instantiate abstract class PluginArgsBuilder" in str(
+            excinfo.value
+        )
+
+class TestPluginBuilderFactory():
+    @pytest.fixture()
+    def plugin_builder_factory(self):
+        return plugin.PluginArgsBuilderFactory()
+
+    def test_defaults(self, plugin_builder_factory):
+        assert plugin_builder_factory._builder is None
+
+        builder = plugin_builder_factory.set_builder()
+        assert isinstance(builder, plugin.CurrentPluginArgsBuilder)
+        assert isinstance(
+            plugin_builder_factory._builder, plugin.CurrentPluginArgsBuilder
+        )
+
+class TestPluginBuilder():
+    @pytest.fixture()
+    def plugin_builder(self):
+        return plugin.CurrentPluginArgsBuilder()
+
+    def test_default(self, plugin_builder, plugin_data_dir):
+        assert isinstance(plugin_builder.matcher, plugin.RepoPluginConfigMatcher)
+        assert plugin_builder.species is None
+        assert plugin_builder.assembly is None
+        assert plugin_builder.version is None
+        assert plugin_builder.base_path == os.path.join(plugin_data_dir, "grch38/eNone/vep/plugin_data")
+
+    def test_match(self, plugin_builder):
+        plugin_builder.species = "homo_sapiens"
+
+        assert plugin_builder.match("CADD")
+        assert plugin_builder.match("Downstream")
+        assert plugin_builder.match("AlphaMissense")
+
+        assert not plugin_builder.match("NonExisting")
+
+    def test_get_args(self, plugin_builder, plugin_data_dir):
+        plugin_builder.species = "homo_sapiens"
+        plugin_builder.assembly = "GRCh38"
+        plugin_builder.version = 114
+
+        assert plugin_builder.get_args("CADD") == {
+            "snv": f"{plugin_data_dir}/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_whole_genome_SNVs.tsv.gz",
+            "indels": f"{plugin_data_dir}/grch38/e114/vep/plugin_data/CADD_GRCh38_1.7_InDels.tsv.gz"
+        }
+
+class TestRepoPluginConfigMatcher():
+    @pytest.fixture()
+    def matcher(self):
+        return plugin.RepoPluginConfigMatcher()
+    
+    def test_defaults(self, matcher, repo_dir):
+        assert matcher.repo_dir == repo_dir
+        assert matcher.config_file == os.path.join(repo_dir, "VEP_plugins", "plugin_config.txt")
+
+    def test_match(self, matcher):
+        species = "homo_sapiens"
+
+        assert matcher.match("CADD", species)
+        assert matcher.match("Downstream", species)
+        assert matcher.match("AlphaMissense", species)
+
+        assert not matcher.match("NonExisting", species)
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/Cargo.lock b/src/rust/ensembl/bed_to_wig/Cargo.lock
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/Cargo.lock
rename to src/rust/ensembl/bed_to_wig/Cargo.lock
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/Cargo.toml b/src/rust/ensembl/bed_to_wig/Cargo.toml
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/Cargo.toml
rename to src/rust/ensembl/bed_to_wig/Cargo.toml
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/src/main.rs b/src/rust/ensembl/bed_to_wig/src/main.rs
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/bed_to_wig/src/main.rs
rename to src/rust/ensembl/bed_to_wig/src/main.rs
diff --git a/src/rust/ensembl/bed_to_wig/test.bw b/src/rust/ensembl/bed_to_wig/test.bw
new file mode 100644
index 00000000..e69de29b
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/merge_bed/Cargo.lock b/src/rust/ensembl/merge_bed/Cargo.lock
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/merge_bed/Cargo.lock
rename to src/rust/ensembl/merge_bed/Cargo.lock
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/merge_bed/Cargo.toml b/src/rust/ensembl/merge_bed/Cargo.toml
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/merge_bed/Cargo.toml
rename to src/rust/ensembl/merge_bed/Cargo.toml
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/merge_bed/src/main.rs b/src/rust/ensembl/merge_bed/src/main.rs
similarity index 100%
rename from nextflow/vcf_prepper/src/rust/ensembl/merge_bed/src/main.rs
rename to src/rust/ensembl/merge_bed/src/main.rs
diff --git a/src/rust/ensembl/vcf_to_bed/Cargo.lock b/src/rust/ensembl/vcf_to_bed/Cargo.lock
new file mode 100644
index 00000000..17b858e8
--- /dev/null
+++ b/src/rust/ensembl/vcf_to_bed/Cargo.lock
@@ -0,0 +1,407 @@
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+checksum = "28d3b2b1366ec20994f1fd18c3c594f05c5dd4bc44d8bb0c1c632c8d6829481f"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a8e94ea7f378bd32cbbd37198a4a91436180c5bb472411e48b5ec2e2124ae9e"
+dependencies = [
+ "serde_core",
+]
+
+[[package]]
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+checksum = "41d385c7d4ca58e59fc732af25c3983b67ac852c1a25000afe1175de458b67ad"
+dependencies = [
+ "serde_derive",
+]
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "serde_json"
+version = "1.0.145"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "402a6f66d8c709116cf22f558eab210f5a50187f702eb4d7e5ef38d9a7f1c79c"
+dependencies = [
+ "itoa",
+ "memchr",
+ "ryu",
+ "serde",
+ "serde_core",
+]
+
+[[package]]
+name = "strsim"
+version = "0.11.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
+
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ede7c438028d4436d71104916910f5bb611972c5cfd7f89b8300a8186e6fada6"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+
+[[package]]
+name = "thiserror"
+version = "1.0.69"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52"
+dependencies = [
+ "thiserror-impl",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "1.0.69"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "unicode-ident"
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f63a545481291138910575129486daeaf8ac54aee4387fe7906919f7830c7d9d"
+
+[[package]]
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+checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "40afbbcfe14b8c3bdaddc8bba0cb32e1d0f2b0b0196a8633ac37a7a000b88035"
+dependencies = [
+ "nom",
+ "once_cell",
+ "thiserror",
+]
+
+[[package]]
+name = "vcf_to_bed"
+version = "0.2.0"
+dependencies = [
+ "clap",
+ "flate2",
+ "serde_json",
+ "vcf",
+]
+
+[[package]]
+name = "windows-link"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "45e46c0661abb7180e7b9c281db115305d49ca1709ab8242adf09666d2173c65"
+
+[[package]]
+name = "windows-sys"
+version = "0.60.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2f500e4d28234f72040990ec9d39e3a6b950f9f22d3dba18416c35882612bcb"
+dependencies = [
+ "windows-targets",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.53.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2d42b7b7f66d2a06854650af09cfdf8713e427a439c97ad65a6375318033ac4b"
+dependencies = [
+ "windows-link",
+ "windows_aarch64_gnullvm",
+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
+
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "86b8d5f90ddd19cb4a147a5fa63ca848db3df085e25fee3cc10b39b6eebae764"
+
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c7651a1f62a11b8cbd5e0d42526e55f2c99886c77e007179efff86c2b137e66c"
+
+[[package]]
+name = "windows_i686_gnu"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c1dc67659d35f387f5f6c479dc4e28f1d4bb90ddd1a5d3da2e5d97b42d6272c3"
+
+[[package]]
+name = "windows_i686_gnullvm"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ce6ccbdedbf6d6354471319e781c0dfef054c81fbc7cf83f338a4296c0cae11"
+
+[[package]]
+name = "windows_i686_msvc"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "581fee95406bb13382d2f65cd4a908ca7b1e4c2f1917f143ba16efe98a589b5d"
+
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2e55b5ac9ea33f2fc1716d1742db15574fd6fc8dadc51caab1c16a3d3b4190ba"
+
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0a6e035dd0599267ce1ee132e51c27dd29437f63325753051e71dd9e42406c57"
+
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.53.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "271414315aff87387382ec3d271b52d7ae78726f5d44ac98b4f4030c91880486"
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.toml b/src/rust/ensembl/vcf_to_bed/Cargo.toml
similarity index 77%
rename from nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.toml
rename to src/rust/ensembl/vcf_to_bed/Cargo.toml
index c7bba79c..c1ffff53 100755
--- a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/Cargo.toml
+++ b/src/rust/ensembl/vcf_to_bed/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "vcf_to_bed"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -9,3 +9,4 @@ edition = "2021"
 vcf="*"
 flate2="*"
 serde_json="*"
+clap= {version="*", features=["derive"]}
\ No newline at end of file
diff --git a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/src/main.rs b/src/rust/ensembl/vcf_to_bed/src/main.rs
similarity index 69%
rename from nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/src/main.rs
rename to src/rust/ensembl/vcf_to_bed/src/main.rs
index 8e12d234..13f64a8d 100755
--- a/nextflow/vcf_prepper/src/rust/ensembl/vcf_to_bed/src/main.rs
+++ b/src/rust/ensembl/vcf_to_bed/src/main.rs
@@ -14,9 +14,25 @@
  * limitations under the License.
  */
  
-use std::{io::{BufReader,Write}, fs::File, env, process::exit, collections::HashMap, collections::HashSet};
-use vcf::{VCFError, VCFReader};
+use std::{io::{BufReader,Write}, fs::File, process::exit, collections::HashMap, collections::HashSet};
+use vcf::{VCFError, VCFReader, VCFHeader};
 use flate2::read::MultiGzDecoder;
+use clap::Parser;
+
+#[derive(Parser, Debug)]
+#[command(version)]
+struct Args {
+    #[arg(short, long, help="VCF file to convert")]
+    vcf: String,
+    #[arg(short, long, help="Output bed file")]
+    output: String,
+    #[arg(short, long, help="JSON file with consequence ranks")]
+    rank: String,
+    #[arg(short, long, help="JSON file specifying required bed fields with metadata")]
+    bed_fields: String,
+    #[arg(short, long, help="VCF contains structural variant")]
+    structural_variant: bool
+}
 
 const VARIANTGROUP : [(&str, u8); 45] = [
     ("frameshift_variant", 1),
@@ -101,6 +117,21 @@ const SV_VARIANTGROUP : [(&str, u8); 32] = [
     ("insertion", 13)
 ];
 
+struct WritableFields {
+    chromosome: bool,
+    start: bool,
+    end: bool,
+    id: bool,
+    variety: bool,
+    reference: bool,
+    alts: bool,
+    group: bool,
+    severity: bool,
+    severity_rank: bool,
+    extent: bool,
+    short_alt: bool
+}
+
 struct Line {
     chromosome: String,
     start: u64,
@@ -112,7 +143,8 @@ struct Line {
     group: u8,
     severity: String,
     severity_rank: u8,
-    extent: u64
+    extent: u64,
+    short_alt: bool
 }
 
 impl Line {
@@ -129,7 +161,7 @@ impl Line {
         self.variety != other.variety 
     }
     
-    fn merge(&mut self, mut more: Option<Line>, out: &mut File) {
+    fn merge(&mut self, mut more: Option<Line>, out: &mut File, wfields: &WritableFields) {
         // merge new line if not empty (and a Line instance)
         if let Some(ref mut more) = more {
             if self.compatible(more) {
@@ -156,18 +188,28 @@ impl Line {
         // print out the current line
         if self.alts.len() > 0 {
             let alts = Vec::from_iter(self.alts.clone());
-            write!(out, "{} {} {} {} {} {} {} {} {}",
-                self.chromosome, self.start, self.end,
-                self.id, self.variety, self.reference,
-                alts.join(","), self.group, self.severity
+            write!(out, "{} {} {} {} {} {} {} {}",
+                self.chromosome, 
+                self.start, 
+                self.end,
+                self.id, 
+                self.variety, 
+                self.reference,
+                alts.join(","), 
+                self.group
             ).unwrap();
-            
-            if self.extent != 0 {
-                write!(out, " {}\n", self.extent).unwrap();
+            // allowing only 3 configurable fields as I don't wanna write lot
+            // of if's - need an efficient way of doing it
+            if wfields.severity { 
+                write!(out, " {}", self.severity).unwrap();
             }
-            else {
-                write!(out, "\n").unwrap();
+            if wfields.extent {
+                write!(out, " {}", self.extent).unwrap();
             }
+            if wfields.short_alt {
+                write!(out, " {}", self.short_alt).unwrap();
+            }
+            write!(out, "\n").unwrap();
         }
         
         // make the new Line as the current one
@@ -177,25 +219,95 @@ impl Line {
     }
 }
 
+fn gen_csq_info_idx(header: &VCFHeader) -> HashMap<&str, usize> {
+    let csq_info_desc = match header.info("CSQ".as_bytes()) {
+        Some(csq_info) => {
+            match str::from_utf8(csq_info.description) {
+                Ok(desc) => desc,
+                Err(_) => {
+                    println!("[ERROR] cannot parse header to get INFO/CSQ");
+                    exit(1);
+                }
+            }
+        },
+        None => {
+            println!("[ERROR] cannot parse header to get INFO/CSQ");
+            exit(1);
+        }
+    };
+    let csq_header_idx: HashMap<&str, usize> = match csq_info_desc.split("Format: ").nth(1) {
+        Some(csq_headers) => {
+            let mut i: usize = 0;
+            let mut tmp_csq_header_idx = HashMap::new();
+            for header in csq_headers.split("|") {
+                tmp_csq_header_idx.insert(header, i);
+                i += 1;
+            }
+
+            tmp_csq_header_idx
+        },
+        None => {
+            println!("[ERROR] cannot parse header to get INFO/CSQ");
+            exit(1);
+        }
+    };
+
+    return csq_header_idx;
+}
+
 fn main() -> Result<(), VCFError> {
     // read cli arguments
-    let args = env::args().collect::<Vec<_>>();
+    let args = Args::parse();
     let mut reader = VCFReader::new(BufReader::new(MultiGzDecoder::new(File::open(
-        &args[1]
+        args.vcf
     )?)))?;
-    let mut out = File::create(&args[2]).unwrap();
-    let json = std::fs::read_to_string(&args[3]).unwrap();
+    let mut out = File::create(args.output).unwrap();
+    let rank = std::fs::read_to_string(args.rank).unwrap();
+    let bed_fields = std::fs::read_to_string(args.bed_fields).unwrap();
+    let is_sv = args.structural_variant;
 
-    let mut is_sv = false;
-    if args.len() == 5 && String::from(&args[4]) == "1" {
-        is_sv = true;
-    }
-        
-    let severity = {
-        serde_json::from_str::<HashMap<String, String>>(&json).unwrap()
+    // generate Hashmap of INFO/CSQ header indexes and retrieve relavant header indexes
+    let header = reader.header();
+    let csq_header_idx: HashMap<&str, usize> = gen_csq_info_idx(&header);
+    let &csqh_conseq_idx = match csq_header_idx.get("Consequence") {
+        Some(idx) => idx,
+        None => {
+            println!("[ERROR] could not determine index of 'Consequence' field from INFO/CSQ");
+            exit(1);
+        }
+    };
+    let &csqh_variant_class_idx = match csq_header_idx.get("VARIANT_CLASS") {
+        Some(idx) => idx,
+        None => {
+            println!("[ERROR] could not determine index of 'VARIANT_CLASS' field from INFO/CSQ");
+            exit(1);
+        }
     };
     
-    // create the severity hash
+    // load bed fields json and map it to writable fields
+    let bfields = serde_json::from_str::<serde_json::Value>(&bed_fields).unwrap();
+    let fields = bfields.get("fields").unwrap();
+    let wfields = WritableFields {
+        chromosome: fields.get("chromosome").is_some(),
+        start: fields.get("start").is_some(),
+        end: fields.get("end").is_some(),
+        id: fields.get("id").is_some(),
+        variety: fields.get("variety").is_some(),
+        reference: fields.get("reference").is_some(),
+        alts: fields.get("alts").is_some(),
+        group: fields.get("group").is_some(),
+        severity: fields.get("severity").is_some(),
+        severity_rank: fields.get("severity_rank").is_some(),
+        extent: fields.get("extent").is_some(),
+        short_alt: fields.get("short_alt").is_some()        
+    };
+
+    // load consequence ranks hash
+    let csq_ranks = {
+        serde_json::from_str::<HashMap<String, String>>(&rank).unwrap()
+    };
+    
+    // load variant group hash
     let mut variant_groups = HashMap::new();
     if is_sv {
         for (csq, value) in &SV_VARIANTGROUP {
@@ -222,12 +334,11 @@ fn main() -> Result<(), VCFError> {
         group: 0,
         severity: "".to_string(),
         severity_rank: 255,
-        extent: 0
+        extent: 0,
+        short_alt: false
     };
     while reader.next_record(&mut record)? {
-        let reference = String::from_utf8(record.reference.clone()).unwrap();
-        let ref_len = reference.len() as u64;
-        
+        // read id:
         let mut multiple_ids = false;
         let ids = record.id.iter().map(|b| {
             String::from_utf8(b.clone())
@@ -243,19 +354,24 @@ fn main() -> Result<(), VCFError> {
             );
             continue; 
         }
+
+        // read ref allele:
+        let reference = String::from_utf8(record.reference.clone()).unwrap();
+        let ref_len = reference.len() as u64;
         
+        // read alt alleles:
         let alts = record.alternative.iter().map(|a| {
             String::from_utf8(a.clone())
         }).collect::<Result<HashSet<_>,_>>().unwrap();
         
-        // TBD: replace hardcoded index value - .nth(1)
+        // read INFO/CSQ/Consequence:
         let csq = record.info(b"CSQ").map(|csqs| {
             csqs.iter().map(|csq| {
                 let s = String::from_utf8_lossy(csq);
-                s.split("|").nth(1).unwrap_or("").to_string()
+                s.split("|").nth(csqh_conseq_idx).unwrap_or("").to_string()
             }).collect::<Vec<String>>()
         }).unwrap_or(vec![]);
-        // if csq is empty we won't have most severe consequence
+        // SKIP if csq is empty
         if csq.is_empty(){  
             println!("[WARNING] INFO/CSQ empty - {0}:{1}, skipping",
                 String::from_utf8(record.chromosome.to_vec()).unwrap(), 
@@ -264,21 +380,22 @@ fn main() -> Result<(), VCFError> {
             continue; 
         }
         
-        // TBD: replace hardcoded index value - .nth(21)
+        // INFO/CSQ/VARIANT_CLASS
         let class = record.info(b"CSQ").map(|csqs| {
             csqs.iter().map(|csq| {
                 let s = String::from_utf8_lossy(csq);
-                s.split("|").nth(21).unwrap_or("").to_string()
+                s.split("|").nth(csqh_variant_class_idx).unwrap_or("").to_string()
             }).collect::<Vec<String>>()
         }).unwrap_or(vec![]);
         
-        // check for SV
+        // check for symbolic alt
         let mut symbolic_alts = false;
+        let mut max_alt_len = 0;
         for alt in alts.iter() {
-            if alt.chars().any(|c| (
-                    c != 'A' && c != 'T' && c != 'C' && c != 'G' && c != 'N'
-                    && c != 'a' && c != 't' && c != 'c' && c != 'g' && c != 'n'
-                )) {
+            if alt.chars().any(|c| 
+                    c != 'A' && c != 'T' && c != 'C' && c != 'G' && c != 'N' &&
+                    c != 'a' && c != 't' && c != 'c' && c != 'g' && c != 'n'
+                ) {
                 symbolic_alts = true;
             }
             if !is_sv && symbolic_alts {
@@ -286,6 +403,11 @@ fn main() -> Result<(), VCFError> {
                     If you are running this script for structural variant please re-run setting the 4th argument field to 1.");
                 exit(1)
             }
+
+            let alt_len = alt.len();
+            if alt_len > max_alt_len {
+                max_alt_len = alt_len;
+            }
         }
 
         for id in ids.iter() {
@@ -293,10 +415,12 @@ fn main() -> Result<(), VCFError> {
             let mut most_severe_csq = "";
             let mut most_severe_csq_rank = 255;
             
-            // calculate most severe consequence and variant group of that consequence
+            /* 
+             * calculate most severe consequence and variant group of that consequence
+             */
             for csq_str in csq.iter() {
                 for csq_here in csq_str.split("&") {
-                    let csq_rank_here = (*severity.get(csq_here).unwrap_or(&String::from("0"))).parse::<u8>().unwrap();
+                    let csq_rank_here = (*csq_ranks.get(csq_here).unwrap_or(&String::from("0"))).parse::<u8>().unwrap();
                     if csq_rank_here < most_severe_csq_rank {
                         variant_group = *variant_groups.get(csq_here).unwrap_or(&0);
                         most_severe_csq = csq_here;
@@ -305,7 +429,9 @@ fn main() -> Result<(), VCFError> {
                 }
             }
             
-            // calcualte variant class - we store it as variety
+            /* 
+             * calculate variant class - we store it as variety
+             */
             // variety should always be same for each variant allele - VEP puts variant class at variant level (using Bio::EnsEMBL::Variation::Utils::Sequence::SO_variation_class)
             // if cannot be deduced the default value is - sequence_alteration
             let mut variety = class[0].to_string();
@@ -344,6 +470,9 @@ fn main() -> Result<(), VCFError> {
                 }
             }
 
+            /*
+             * calculate positions
+             */
             // start position in bed is 0-indexed
             let mut start = record.position - 1;
         
@@ -354,12 +483,22 @@ fn main() -> Result<(), VCFError> {
                 end = start;
             }
 
-            // for short variants we do not use extent
+            /*
+             * particular calculation for SV
+             *  - update variant group and position for SVs
+             *  - if non-symbolic set is_sv = false for alt bp < 50
+             *  - calculate extent 
+             */
             let mut extent = 0;
-            
+            let mut short_alt = false;
+         
             if is_sv {
                 // overwrite variant group to come from variant class instead of consequence
                 variant_group = *variant_groups.get(&variety).unwrap_or(&0);
+
+                if !symbolic_alts && max_alt_len < 50 {
+                    short_alt = true;
+                }
                 
                 // check INFO/SVLEN or INFO/END to get the end position
                 let svlens = record.info(b"SVLEN").map(|svlen| {
@@ -429,13 +568,14 @@ fn main() -> Result<(), VCFError> {
                 group: variant_group,
                 severity: most_severe_csq.to_string(),
                 severity_rank: most_severe_csq_rank,
-                extent: extent
+                extent: extent,
+                short_alt: short_alt
             };
             
-            lines.merge(Some(more), &mut out);
+            lines.merge(Some(more), &mut out, &wfields);
         }
     }
     
-    lines.merge(None, &mut out);
+    lines.merge(None, &mut out, &wfields);
     Ok(())
 }
\ No newline at end of file