parabricks/applybqsr version updated and tests migrated to nf-test

.github/workflows/test.yml

@@ -344,14 +344,10 @@ jobs:
             tags: nanoplot
           - profile: conda
             tags: ncbitools/vecscreen
-          - profile: conda
-            tags: parabricks/applybqsr
           - profile: conda
             tags: parabricks/dbsnp
           - profile: conda
             tags: parabricks/deepvariant
-          - profile: conda
-            tags: parabricks/fq2bam
           - profile: conda
             tags: parabricks/genotypegvcf
           - profile: conda
@@ -648,18 +644,6 @@ jobs:
             path: modules/nf-core/islandpath
           - profile: conda
             path: modules/nf-core/scimap/mcmicro
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: docker_self_hosted
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: singularity
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bam
-          - profile: docker_self_hosted
-            path: modules/nf-core/parabricks/fq2bam
-          - profile: singularity
-            path: modules/nf-core/parabricks/fq2bam
           - profile: conda
             path: subworkflows/nf-core/vcf_annotate_ensemblvep
           - profile: conda
@@ -672,6 +656,9 @@ jobs:
             path: subworkflows/nf-core/fastq_align_bwa
           - profile: conda
             path: subworkflows/nf-core/fasta_newick_epang_gappa
+          - path: modules/nf-core/parabricks/fq2bammeth
+          - path: modules/nf-core/parabricks/fq2bam
+          - path: modules/nf-core/parabricks/applybqsr
           - profile: conda
             path: modules/nf-core/xeniumranger/relabel
           - profile: conda
@@ -786,6 +773,131 @@ jobs:
         run: |
           sudo rm -rf /home/ubuntu/tests/
 
+  nf-test-gpu:
+    runs-on: ${{ github.event.inputs.runners  || 'gpu' }}
+    name: nf-test with GPUs
+    needs: [nf-test-changes]
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    strategy:
+      fail-fast: false
+      matrix:
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [conda, docker_self_hosted, singularity]
+        include:
+          - path: modules/nf-core/parabricks/applybqsr
+          - path: modules/nf-core/parabricks/fq2bam
+          # - path: modules/nf-core/parabricks/fq2bammeth excluded - tackle in different PR
+        exclude:
+          - profile: conda
+            path: modules/nf-core/parabricks/fq2bam
+          - profile: conda
+            path: modules/nf-core/parabricks/fq2bammeth
+          - profile: conda
+            path: modules/nf-core/parabricks/applybqsr
+    env:
+      NXF_ANSI_LOG: false
+      NFTEST_VER: "0.9.0"
+      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
+      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
+
+      - name: Setup 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: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+          restore-keys: |
+            ${{ runner.os }}-pip-pdiff
+
+      - name: Install Python dependencies
+        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
+          channels: conda-forge,bioconda
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        # TODO Only run if the tag includes `sentieon`
+        if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
+        run: |
+          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")
+      # Test the module
+      - name: Run nf-test
+        if: ${{ matrix.path != '' }}
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
+          SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        run: |
+          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
+          if [ "${{ matrix.profile }}" == "docker" ]; then
+            PROFILE="docker_self_hosted"
+          else
+            PROFILE=${{ matrix.profile }}
+          fi
+
+          NFT_WORKDIR=~ \
+          nf-test test \
+            --profile=${{ matrix.profile }},gpu \
+            --tap=test.tap \
+            --verbose \
+            ${{ matrix.path }}
+
+      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+        if: ${{ matrix.path != '' }}
+        with:
+          path: >-
+            test.tap
+
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/
+
   confirm-pass:
     runs-on: ubuntu-latest
     needs:

modules/nf-core/parabricks/applybqsr/main.nf

@@ -1,12 +1,16 @@
 process PARABRICKS_APPLYBQSR {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
 
-    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"
 
     input:
-    tuple val(meta), path(bam), path(bam_index), path(bqsr_table), path(intervals)
-    tuple val(meta2), path(fasta)
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bam_index)
+    tuple val(meta3), path(bqsr_table)
+    tuple val(meta4), path(intervals)
+    tuple val(meta5), path(fasta)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -25,6 +29,7 @@ process PARABRICKS_APPLYBQSR {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
     def copy_index_command = bam_index ? "cp -L $bam_index `readlink -f $bam`.bai" : ""
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     # parabricks complains when index is not a regular file in the same directory as the bam
     # copy the index to this path.
@@ -38,7 +43,7 @@ process PARABRICKS_APPLYBQSR {
         $interval_command \\
         --out-bam ${prefix}.bam \\
         --num-threads $task.cpus \\
-        --num-gpus $task.accelerator.request \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/parabricks/applybqsr/meta.yml

@@ -23,18 +23,33 @@ input:
         type: file
         description: BAM file
         pattern: "*.bam"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - bam_index:
         type: file
         description: BAM index file
         pattern: "*.bai"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - bqsr_table:
         type: file
         description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.
         pattern: "*.table"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - intervals:
         type: file
         description: intervals
-  - - meta2:
+  - - meta5:
         type: map
         description: |
           Groovy Map containing sample information