configure Dependabot for Dockerfile and add auto-sync workflow

.github/dependabot.yml

@@ -9,11 +9,12 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
-    target-branch: "module-profile"
+    target-branch: "main"
+
   - package-ecosystem: "docker"
     directories:
       - "/env/picard"
       - "/env/bases2fastq"
     schedule:
       interval: "daily"
-    target-branch: "module-profile"
+    target-branch: "main"

.github/workflows/update-nextflow-on-dependabot.yml

@@ -0,0 +1,103 @@
+name: Update nextflow.config on Dependabot Docker PR
+
+on:
+  pull_request_target:
+    types: [opened, reopened, synchronize]
+    paths:
+      - 'env/picard/Dockerfile'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-nextflow-config:
+    if: github.actor == 'dependabot[bot]'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout PR HEAD safely
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          persist-credentials: false
+
+      - name: Parse image & version from env/picard/Dockerfile
+        id: parse
+        shell: bash
+        run: |
+          set -euo pipefail
+          DOCKERFILE="env/picard/Dockerfile"
+          if [[ ! -f "$DOCKERFILE" ]]; then
+            echo "skip=true" >>"$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          FULL_IMAGE="$(awk '/^FROM[[:space:]]+/ {print $2; exit}' "$DOCKERFILE")"
+          if [[ -z "${FULL_IMAGE:-}" ]]; then
+            echo "Could not parse FROM line in $DOCKERFILE"; exit 1
+          fi
+
+          IMAGE_BASE="${FULL_IMAGE%%:*}"
+          NEW_TAG="${FULL_IMAGE#*:}"
+
+          echo "image_base=$IMAGE_BASE" >>"$GITHUB_OUTPUT"
+          echo "new_tag=$NEW_TAG" >>"$GITHUB_OUTPUT"
+          echo "skip=false" >>"$GITHUB_OUTPUT"
+
+      - name: Update nextflow.config
+        if: steps.parse.outputs.skip == 'false'
+        shell: bash
+        run: |
+          set -euo pipefail
+          CONFIG_FILE="nextflow.config"
+          IMAGE_BASE="${{ steps.parse.outputs.image_base }}"
+          NEW_TAG="${{ steps.parse.outputs.new_tag }}"
+
+          if [[ ! -f "$CONFIG_FILE" ]]; then
+            echo "Missing $CONFIG_FILE"; exit 1
+          fi
+
+          BEFORE_HASH="$(sha256sum "$CONFIG_FILE" | awk '{print $1}')"
+
+          # 1) container = 'base:anything'  (single or double quotes)
+          sed -i -E "s|(container[[:space:]]*=[[:space:]]*['\"])${IMAGE_BASE}:[^'\"]*(['\"])|\1${IMAGE_BASE}:${NEW_TAG}\2|g" "$CONFIG_FILE"
+
+          # 2) process.container = 'base:anything'
+          sed -i -E "s|(process\.container[[:space:]]*=[[:space:]]*['\"])${IMAGE_BASE}:[^'\"]*(['\"])|\1${IMAGE_BASE}:${NEW_TAG}\2|g" "$CONFIG_FILE"
+
+          # 3) Any stray appearances of base:tag (quote-agnostic), last-resort generic swap
+          sed -i -E "s|(${IMAGE_BASE}:)[0-9A-Za-z._-]+|\1${NEW_TAG}|g" "$CONFIG_FILE"
+
+          AFTER_HASH="$(sha256sum "$CONFIG_FILE" | awk '{print $1}')"
+
+          if [[ "$BEFORE_HASH" == "$AFTER_HASH" ]]; then
+            echo "No container reference to update in $CONFIG_FILE for base ${IMAGE_BASE}."
+            echo "Likely the image is referenced elsewhere or via a param; skipping commit."
+            exit 0
+          fi
+
+          echo "=== Diff ==="
+          git --no-pager diff -- "$CONFIG_FILE" || true
+
+      - name: Commit & push back to PR branch
+        if: steps.parse.outputs.skip == 'false'
+        shell: bash
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -euo pipefail
+          if git diff --quiet -- nextflow.config; then
+            echo "No changes to commit."
+            exit 0
+          fi
+
+          git config user.name  "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add nextflow.config
+          git commit -m "chore(nextflow): sync container tag with Dockerfile (${GITHUB_SHA::7})"
+
+          PR_HEAD="${{ github.event.pull_request.head.ref }}"
+          REPO="${{ github.repository }}"
+          git push "https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${REPO}.git" "HEAD:${PR_HEAD}"

env/picard/Dockerfile

@@ -0,0 +1,3 @@
+FROM broadinstitute/picard:1.0
+
+CMD ["/bin/bash"]

modules/basecall.nf

@@ -0,0 +1,58 @@
+process BASECALL {
+    publishDir "${params.alpha}/logs/${params.fcid}/basecall/${lane}", mode:'copy', failOnError: true, pattern: '.command.*'
+    tag "${params.fcid}"
+
+    module params.PICARD_MODULE
+    module params.JDK_MODULE
+
+    input:
+    val lane
+
+    output:
+    val(lane), emit: lane
+    path(".command.*")
+
+    shell:
+    '''
+    read_structure=$(python3 -c "
+    import xml.dom.minidom
+
+    read_structure = ''
+    runinfo = xml.dom.minidom.parse('!{params.run_dir_path}/RunInfo.xml')
+    nibbles = runinfo.getElementsByTagName('Read')
+
+    for nib in nibbles:
+        read_structure += nib.attributes['NumCycles'].value + 'T'
+
+    print(read_structure)
+    ")
+
+    run_barcode=$(python3 -c "
+    print('!{params.run_dir_path}'.split('_')[-2].lstrip('0'))
+    ")
+
+    out_path="!{params.alpha}/lane/!{params.fcid}/!{lane}"
+    mkdir -p $out_path
+
+    tmp_work_dir="!{params.tmp_dir}!{params.fcid}/!{lane}"
+    mkdir -p $tmp_work_dir
+
+    java -jar -Xmx58g $PICARD_JAR IlluminaBasecallsToFastq \
+        LANE=!{lane} \
+        READ_STRUCTURE=${read_structure} \
+        BASECALLS_DIR=!{params.run_dir_path}/Data/Intensities/BaseCalls \
+        OUTPUT_PREFIX=${out_path}/!{params.fcid}_l0!{lane} \
+        RUN_BARCODE=${run_barcode} \
+        MACHINE_NAME=!{params.seq_id} \
+        FLOWCELL_BARCODE=!{params.fcid} \
+        NUM_PROCESSORS=!{task.cpus} \
+        APPLY_EAMSS_FILTER=false \
+        INCLUDE_NON_PF_READS=false \
+        MAX_READS_IN_RAM_PER_TILE=200000 \
+        MINIMUM_QUALITY=2 \
+        COMPRESS_OUTPUTS=true \
+        TMP_DIR=${tmp_work_dir}
+
+    rm -rf ${tmp_work_dir}
+    '''
+}

modules/check_no_demux.nf

@@ -0,0 +1,17 @@
+process CHECK_NO_DEMUX {
+    tag "${params.fcid}"
+    echo true
+
+    input:
+    val lane
+
+    output:
+    tuple val(lane), env(no_demux), emit: lane
+
+    shell:
+    '''
+    export PYTHONPATH=$PYTHONPATH:!{workflow.projectDir}/bin
+    no_demux=$(python3 -c "from slime import check_demux;r=check_demux('!{params.fcid}', !{lane});print(str(r).lower())")
+    echo "check_no_demux: lane: !{lane}, no_demux: $no_demux"
+    '''
+}

modules/rsync_to_archive.nf

@@ -0,0 +1,21 @@
+process RSYNC_TO_ARCHIVE {
+    publishDir "${params.alpha}/logs/${params.fcid}/archive/rsync/", mode:'copy', failOnError: true
+    tag "${params.fcid}"
+    echo true
+
+    input:
+    path SRC
+    val destination
+
+    output:
+    path(".command.*")
+    env(exit_code), emit: exit_code
+
+    shell:
+    '''
+    echo "rsyncToArchive: SRC: !{SRC}, destination: !{destination}"
+    ssh -i $HOME/.ssh/id_rsa core2 "mkdir -p !{destination}"
+    rsync --copy-links --progress -r -e "ssh -i ${HOME}/.ssh/id_rsa" !{SRC} core2:!{destination}/.
+    exit_code=$?
+    '''
+}

nextflow.config.template → nextflow.config

@@ -118,3 +118,61 @@ trace {
 env {
   SEQERA_ACCESS_TOKEN=""
 }
+
+profiles {
+    hpc-modules {
+        process {
+            withName: 'multiqc' {
+                module = params.MULTIQC_MODULE
+            }  
+            withName: 'tar' {
+                module = params.PBZIP2_MODULE
+            } 
+            withName: '_basecall_bases2fastq' {
+                module = params.BASES2FASTQ_MODULE
+            }
+            withName: '_basecall_picard' {
+                module = params.PICARD_MODULE
+                module = params.JDK_MODULE
+            }
+        }
+    }
+
+    hpc-container {
+        singularity.enabled = true
+
+        process {
+            container = /path/to/conda-container
+
+            withName: '_basecall_picard' {
+                container = 'docker://broadinstitute/picard:2.23.8'
+            }
+
+            withName: 'bases2fastq' {
+                container = 'docker://elembio/bases2fastq:2.2.0
+            }
+        }
+    }
+
+    default {
+        singularity.enabled = true
+
+        conda.enabled = true
+        #conda.cacheDir = 
+        #conda.useMamba = true
+
+
+        process {
+            conda = ${baseDir}/environment.yml
+
+            withName: '_basecall_picard' {
+                container = 'docker://broadinstitute/picard:1.0'
+            }
+
+            withName: 'bases2fastq' {
+                container = 'docker://elembio/bases2fastq:2.1.0'
+            }
+
+        }
+    }
+}