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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -12,8 +12,15 @@ on: | |
| - dev | ||
|
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| env: | ||
| NFT_DIFF: "pdiff" | ||
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | ||
| NFT_VER: "0.9.0" | ||
| NFT_WORKDIR: "~" | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.1" | ||
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | ||
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
|
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| # Cancel if a newer run is started | ||
| concurrency: | ||
|
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@@ -28,7 +35,7 @@ jobs: | |
| # Expose matched filters as job 'tags' output variable | ||
| tags: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
|
||
| - uses: frouioui/paths-filter@main | ||
| id: filter | ||
|
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@@ -63,24 +70,20 @@ jobs: | |
| - tags: "sentieon/haplotyper_skip_filter" | ||
| - NXF_VER: "latest-everything" | ||
| tags: "joint_germline" | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b | ||
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
|
||
| - name: Hash Github Workspace | ||
| id: hash_workspace | ||
| run: | | ||
| echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | ||
| with: | ||
| python-version: "3.x" | ||
| python-version: "3.11" | ||
| cache: "pip" | ||
| cache-dependency-path: | | ||
| **/requirements.txt | ||
|
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@@ -93,30 +96,43 @@ jobs: | |
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
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||
| - name: Setup apptainer | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-apptainer@main | ||
|
|
||
| - name: Set up Singularity | ||
| if: matrix.profile == 'singularity' | ||
| uses: eWaterCycle/setup-singularity@v5 | ||
| with: | ||
| singularity-version: 3.7.1 | ||
| run: | | ||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
| - name: Set up miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | ||
| with: | ||
| miniconda-version: "latest" | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
| 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 | ||
| - name: Cache test data | ||
| id: cache-testdata | ||
| uses: actions/cache@v3 | ||
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | ||
| with: | ||
| path: test-datasets/ | ||
| key: ${{ steps.hash_workspace.outputs.digest }} | ||
|
|
||
| - name: Check out test data | ||
| if: steps.cache-testdata.outputs.cache-hit != 'true' | ||
| uses: actions/checkout@v4 | ||
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: sarek3 | ||
|
|
@@ -164,16 +180,17 @@ jobs: | |
| - name: Upload logs on failure | ||
| if: failure() | ||
| uses: actions/upload-artifact@v2 | ||
| uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4 | ||
| with: | ||
| name: logs-${{ matrix.profile }} | ||
| path: | | ||
| /home/runner/pytest_workflow_*/*/.nextflow.log | ||
| /home/runner/pytest_workflow_*/*/log.out | ||
| /home/runner/pytest_workflow_*/*/log.err | ||
| /home/runner/pytest_workflow_*/*/work | ||
| !/home/runner/pytest_workflow_*/*/work/conda | ||
| !/home/runner/pytest_workflow_*/*/work/singularity | ||
| /home/ubuntu/pytest_workflow_*/*/.nextflow.log | ||
| /home/ubuntu/pytest_workflow_*/*/log.out | ||
| /home/ubuntu/pytest_workflow_*/*/log.err | ||
| /home/ubuntu/pytest_workflow_*/*/work | ||
| !/home/ubuntu/pytest_workflow_*/*/work/conda | ||
| !/home/ubuntu/pytest_workflow_*/*/work/singularity | ||
| !${{ github.workspace }}/.singularity | ||
| nftest-changes: | ||
| name: Check for changes (nf-test) | ||
|
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@@ -182,15 +199,12 @@ jobs: | |
| tags: ${{ steps.filter.outputs.changes }} | ||
|
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||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
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||
| - name: Combine all tags.yml files | ||
| id: get_tags | ||
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | ||
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| - name: debug | ||
| run: cat .github/tags.yml | ||
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| - uses: frouioui/paths-filter@main | ||
| id: filter | ||
| with: | ||
|
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@@ -227,13 +241,16 @@ jobs: | |
| - tags: "cnvkit/antitarget" | ||
| - tags: "cnvkit/batch" | ||
| - tags: "cnvkit/reference" | ||
| - tags: "deepvariant" | ||
| - tags: "controlfreec/assesssignificance" | ||
| - tags: "controlfreec/freec" | ||
| - tags: "deepvariant/rundeepvariant" | ||
| - tags: "dragmap/align" | ||
| - tags: "dragmap/hashtable" | ||
| - tags: "ensemblvep/download" | ||
| - tags: "ensemblvep/vep" | ||
| - tags: "fastp" | ||
| - tags: "fastqc" | ||
| - tags: "fgbio/callmolecularconsensusreads" | ||
| - tags: "fgbio/fastqtobam" | ||
| - tags: "freebayes" | ||
| - tags: "gatk4/applybqsr" | ||
|
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@@ -247,34 +264,30 @@ jobs: | |
| - tags: "gatk4spark/applybqsr" | ||
| - tags: "gatk4spark/markduplicates" | ||
| - tags: "gawk" | ||
| - tags: "lofreq/callparallel" | ||
| - tags: "mosdepth" | ||
| - tags: "multiqc" | ||
| - tags: "ngscheckmate/ncm" | ||
| - tags: "samblaster" | ||
| - tags: "samtools/convert" | ||
| - tags: "samtools/mpileup" | ||
| - tags: "samtools/stats" | ||
| - tags: "sentieon/bwamem" | ||
| - tags: "sentieon/haplotyper" | ||
| - tags: "snpeff/snpeff" | ||
| - tags: "spring/decompress" | ||
| - tags: "strelka/germline" | ||
| - tags: "strelka/somatic" | ||
| - tags: "subworkflows/utils_nfvalidation_plugin" | ||
| - tags: "tabix/bgziptabix" | ||
| - tags: "tabix/tabix" | ||
| - tags: "tiddit/sv" | ||
| - tags: "untar" | ||
| - tags: "pipeline_sarek" | ||
| include: | ||
| - tags: "pipeline_sarek" | ||
| profile: "test,docker" | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
|
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||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
|
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||
| - uses: actions/setup-java@v3 | ||
| - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 | ||
| with: | ||
| distribution: "temurin" | ||
| java-version: "17" | ||
|
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@@ -284,20 +297,10 @@ jobs: | |
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
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| - name: Cache nf-test installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest | ||
|
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||
| - name: Install nf-test | ||
| if: steps.cache-software.outputs.cache-hit != 'true' | ||
| run: | | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash | ||
| sudo mv nf-test /usr/local/bin/ | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: ${{ env.NFT_VER }} | ||
|
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||
| - name: Setup apptainer | ||
| if: matrix.profile == 'singularity' | ||
|
|
@@ -310,22 +313,23 @@ jobs: | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
| - name: Set up miniconda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | ||
| with: | ||
| miniconda-version: "latest" | ||
| auto-update-conda: true | ||
| channels: conda-forge,bioconda,defaults | ||
| python-version: ${{ matrix.python-version }} | ||
| 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) >> $GITHUB_PATH | ||
| # Set up secrets | ||
| # Set up secrets | ||
| - name: Set up nextflow secrets | ||
| if: env.SENTIEON_LICENSE_BASE64 != null | ||
| run: | | ||
|
|
@@ -340,13 +344,15 @@ jobs: | |
| - name: Disk space cleanup | ||
| uses: jlumbroso/[email protected] | ||
|
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| # Test the module | ||
| # Test the component | ||
| - name: Run nf-test | ||
| run: | | ||
| nf-test test \ | ||
| --profile=${{ matrix.profile }} \ | ||
| --profile="+${{ matrix.profile }}" \ | ||
| --tag ${{ matrix.tags }} \ | ||
| --tap=test.tap \ | ||
| --junitxml=test.xml \ | ||
| --debug \ | ||
| --verbose | ||
| confirm-pass: | ||
|
|
||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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