adding github workflow to run nf-test tests

Author: alpae

.github/workflows/nf-test.yml

@@ -0,0 +1,162 @@
+name: nf-test CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+env:
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5"
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - "24.10.2"
+          - "latest-everything"
+        filter: ["workflow", "pipeline"]
+        # filter: ["process", "workflow", "function", "pipeline"]
+        profile: ["conda", "docker", "singularity"]
+        shard: [1, 2, 3, 4, 5]
+        #isMaster:
+        #  - ${{ github.base_ref == 'main' }}
+        #exclude:
+        #  - isMaster: false
+        #    profile: "conda"
+        #  - isMaster: false
+        #    profile: "singularity"
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - name: Set up apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Cache pdiff
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+
+      - name: Install pdiff
+        run: python -m pip install --upgrade pip pdiff cryptography
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
+
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
+        run: |
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@v1.3.1
+
+      - name: Start summary
+        id: print-test
+        run: |
+          echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "This \`${{ matrix.filter }}\` ${{ matrix.shard }}/5 shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          nf-test test \
+            --ci \
+            --dryRun \
+            --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+            --shard ${{ matrix.shard }}/5 \
+            --changed-since HEAD^ \
+            --follow-dependencies \
+            --profile "+${{ matrix.profile }}" \
+            --filter ${{ matrix.filter }} \
+            | grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY
+
+      - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5"
+        run: |
+          nf-test test \
+              --ci \
+              --debug \
+              --verbose \
+              --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
+              --shard ${{ matrix.shard }}/5 \
+              --changed-since HEAD^ \
+              --follow-dependencies \
+              --profile "+${{ matrix.profile }}" \
+              --filter ${{ matrix.filter }}
+
+      - name: Print success in summary
+        if: success()
+        run: |
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "All test(s) successfull :tada:" >> $GITHUB_STEP_SUMMARY
+
+      - name: Print failure in summary
+        if: failure()
+        run: |
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "Some test(s) failed :cold_sweat:" >> $GITHUB_STEP_SUMMARY
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: "TEST-*.xml"
+
+      - name: Clean up
+        if: success() || failure()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/