DESeq2 and Limma can be a low-resource processes (#4423) #5
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
| name: Run tests | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| prettier: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: self-hosted | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| pytest-changes: | |
| name: pytest-changes | |
| runs-on: self-hosted | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - name: Combine all tags.yml files | |
| id: get_tags | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| token: "" | |
| nf-core-lint: | |
| runs-on: self-hosted | |
| name: nf-core-lint | |
| needs: [pytest-changes, nf-test-changes] | |
| if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: | |
| [ | |
| "${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
| "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint module ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| if: ${{ !startsWith(matrix.tags, 'subworkflows/') }} | |
| - name: Remove substring from matrix.tags | |
| id: remove_substring | |
| run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT | |
| - name: Lint subworkflow ${{ matrix.tags }} | |
| run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}} | |
| if: ${{ startsWith(matrix.tags, 'subworkflows/') }} | |
| migration: | |
| runs-on: ubuntu-latest | |
| name: nf-test Migration Notice | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.modules != '[]' | |
| # Needed for Deprecation comment | |
| permissions: | |
| pull-requests: write | |
| steps: | |
| - name: Migration Comment | |
| uses: mshick/add-pr-comment@v2 | |
| if: ${{ github.event_name == 'pull_request' }} | |
| with: | |
| message: | | |
| Hello! | |
| We're in the process of migrating to [nf-test](https://code.askimed.com/nf-test)!🚀 | |
| We would appreciate this test being rewritten in nf-test. | |
| We have documented a step-by-step process to do so [here](https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test). | |
| If you aren't able to do that right now [raise an issue](https://github.com/nf-core/modules/issues/new?assignees=&labels=bug&projects=&template=bug_report.yml). | |
| pytest: | |
| runs-on: ubuntu-latest | |
| name: pytest | |
| needs: [pytest-changes] | |
| if: needs.pytest-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: happy/sompy | |
| - profile: "conda" | |
| tags: cellpose | |
| - profile: "conda" | |
| tags: mcquant | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: backsub | |
| - profile: "conda" | |
| tags: basicpy | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: bwa/aln | |
| - profile: "conda" | |
| tags: bwa/index | |
| - profile: "conda" | |
| tags: bwa/mem | |
| - profile: "conda" | |
| tags: bwa/sampe | |
| - profile: "conda" | |
| tags: bwa/samse | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: cellranger/mkvdjref | |
| - profile: "conda" | |
| tags: cellranger/multi | |
| - profile: "conda" | |
| tags: cellranger/vdj | |
| - profile: "conda" | |
| tags: cellrangeratac/count | |
| - profile: "conda" | |
| tags: cellrangeratac/mkfastq | |
| - profile: "conda" | |
| tags: cellrangeratac/mkref | |
| - profile: "conda" | |
| tags: coreograph | |
| - profile: "conda" | |
| tags: deepcell/mesmer | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastani | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: gatk4/germlinecnvcaller | |
| - profile: "conda" | |
| tags: gatk4/postprocessgermlinecnvcalls | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: hlala/preparegraph | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: medaka | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: minimap2/align | |
| - profile: "conda" | |
| tags: mitohifi/mitohifi | |
| - profile: "conda" | |
| tags: mitohifi/findmitoreference | |
| - profile: "conda" | |
| tags: nanoplot | |
| - profile: "conda" | |
| tags: ncbitools/vecscreen | |
| - profile: "conda" | |
| tags: parabricks/applybqsr | |
| - profile: "conda" | |
| tags: parabricks/fq2bam | |
| - profile: "conda" | |
| tags: picard/collecthsmetrics | |
| - profile: "conda" | |
| tags: picard/collectwgsmetrics | |
| - profile: "conda" | |
| tags: scimap/mcmicro | |
| - profile: "conda" | |
| tags: sentieon/applyvarcal | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: sentieon/datametrics | |
| - profile: "conda" | |
| tags: sentieon/dedup | |
| - profile: "conda" | |
| tags: sentieon/dnamodelapply | |
| - profile: "conda" | |
| tags: sentieon/dnascope | |
| - profile: "conda" | |
| tags: sentieon/gvcftyper | |
| - profile: "conda" | |
| tags: sentieon/haplotyper | |
| - profile: "conda" | |
| tags: sentieon/readwriter | |
| - profile: "conda" | |
| tags: sentieon/tnfilter | |
| - profile: "conda" | |
| tags: sentieon/tnhaplotyper2 | |
| - profile: "conda" | |
| tags: sentieon/tnscope | |
| - profile: "conda" | |
| tags: sentieon/varcal | |
| - profile: "conda" | |
| tags: sentieon/wgsmetrics | |
| - profile: "conda" | |
| tags: spaceranger/count | |
| - profile: "conda" | |
| tags: spaceranger/mkgtf | |
| - profile: "conda" | |
| tags: spaceranger/mkref | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "conda" | |
| tags: vt/decompose | |
| - profile: "singularity" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: subworkflows/bcl_demultiplex | |
| - profile: "conda" | |
| tags: subworkflows/fasta_clean_fcs | |
| - profile: "conda" | |
| tags: islandpath | |
| - profile: "conda" | |
| tags: subworkflows/bam_qc_picard | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow cryptography | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_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 miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| 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 | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run pytest-workflow | |
| # only use one thread for pytest-workflow to avoid race condition on conda cache. | |
| run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt-get update > /dev/null | |
| sudo apt-get install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Setting global variables | |
| uses: actions/github-script@v6 | |
| id: parsed | |
| with: | |
| script: | | |
| return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') | |
| result-encoding: string | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} | |
| 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 | |
| !${{ github.workspace }}/.singularity | |
| nf-test: | |
| runs-on: ubuntu-latest | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| profile: ["docker", "singularity", "conda"] | |
| exclude: | |
| - tags: "nf-test" | |
| - profile: "conda" | |
| tags: annotsv | |
| - profile: "conda" | |
| tags: happy/sompy | |
| - profile: "conda" | |
| tags: backsub | |
| - profile: "conda" | |
| tags: bases2fastq | |
| - profile: "conda" | |
| tags: bcl2fastq | |
| - profile: "conda" | |
| tags: bclconvert | |
| - profile: "conda" | |
| tags: cellranger/count | |
| - profile: "conda" | |
| tags: cellranger/mkfastq | |
| - profile: "conda" | |
| tags: cellranger/mkgtf | |
| - profile: "conda" | |
| tags: cellranger/mkref | |
| - profile: "conda" | |
| tags: custom/dumpsoftwareversions | |
| - profile: "conda" | |
| tags: deepvariant | |
| - profile: "conda" | |
| tags: ensemblvep/vep | |
| - profile: "conda" | |
| tags: fastk/fastk | |
| - profile: "conda" | |
| tags: fastk/histex | |
| - profile: "conda" | |
| tags: fastk/merge | |
| - profile: "conda" | |
| tags: fcs/fcsadaptor | |
| - profile: "conda" | |
| tags: fcs/fcsgx | |
| - profile: "conda" | |
| tags: gatk4/cnnscorevariants | |
| - profile: "conda" | |
| tags: gatk4/determinegermlinecontigploidy | |
| - profile: "conda" | |
| tags: genescopefk | |
| - profile: "conda" | |
| tags: ilastik/multicut | |
| - profile: "conda" | |
| tags: ilastik/pixelclassification | |
| - profile: "conda" | |
| tags: imputeme/vcftoprs | |
| - profile: "conda" | |
| tags: merquryfk/katcomp | |
| - profile: "conda" | |
| tags: merquryfk/katgc | |
| - profile: "conda" | |
| tags: merquryfk/merquryfk | |
| - profile: "conda" | |
| tags: merquryfk/ploidyplot | |
| - profile: "conda" | |
| tags: sentieon/bwaindex | |
| - profile: "conda" | |
| tags: sentieon/bwamem | |
| - profile: "conda" | |
| tags: universc | |
| - profile: "singularity" | |
| tags: universc | |
| - profile: "conda" | |
| tags: vt/decompose | |
| - profile: "conda" | |
| tags: subworkflows/vcf_annotate_ensemblvep | |
| env: | |
| NXF_ANSI_LOG: false | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| NFTEST_VER: "0.8.1" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - 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 | |
| - 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/ | |
| - 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 miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| 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 | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| # Test the module | |
| - name: Run nf-test | |
| run: | | |
| NXF_TEST_DIR=~ \ | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap \ | |
| --verbose | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap | |
| confirm-pass: | |
| runs-on: self-hosted | |
| needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |