Use new nf-test features #2656
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| name: Run nf-test | ||
| on: | ||
| pull_request: | ||
| branches: [master] | ||
| merge_group: | ||
| types: [checks_requested] | ||
| branches: [master] | ||
| workflow_dispatch: | ||
| inputs: | ||
| runners: | ||
| description: "Runners to test on" | ||
| type: choice | ||
| options: | ||
| - "ubuntu-latest" | ||
| - "self-hosted" | ||
| default: "self-hosted" | ||
| # 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: | ||
| nf-test: | ||
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | ||
| name: nf-test | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| shard: [1, 2, 3] | ||
| profile: [conda, docker_self_hosted, singularity] | ||
| filter: [module, workflow] | ||
| exclude: | ||
| - path: modules/nf-core/nf-test | ||
|
Check failure on line 39 in .github/workflows/nf-test.yml
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||
| - profile: conda | ||
| path: modules/nf-core/angsd/gl | ||
| - profile: conda | ||
| path: modules/nf-core/annotsv/installannotations | ||
| - profile: conda | ||
| path: modules/nf-core/happy/sompy | ||
| - profile: conda | ||
| path: modules/nf-core/backsub | ||
| - profile: conda | ||
| path: modules/nf-core/bakta/bakta | ||
| - profile: conda | ||
| path: modules/nf-core/bakta/baktadbdownload | ||
| - profile: conda | ||
| path: modules/nf-core/bases2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/bcl2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/bclconvert | ||
| - profile: conda | ||
| path: modules/nf-core/celesta | ||
| - profile: conda | ||
| path: modules/nf-core/cellpose | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/count | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkfastq | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkgtf | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkref | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/mkvdjref | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/multi | ||
| - profile: conda | ||
| path: modules/nf-core/cellranger/vdj | ||
| - profile: conda | ||
| path: modules/nf-core/checkqc | ||
| - profile: conda | ||
| path: modules/nf-core/custom/dumpsoftwareversions | ||
| - profile: conda | ||
| path: modules/nf-core/deepcell/mesmer | ||
| - profile: conda | ||
| path: modules/nf-core/deepvariant | ||
| - profile: conda | ||
| path: modules/nf-core/ensemblvep/vep | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/fastk | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/histex | ||
| - profile: conda | ||
| path: modules/nf-core/fastk/merge | ||
| - profile: conda | ||
| path: modules/nf-core/fcs/fcsadaptor | ||
| - profile: conda | ||
| path: modules/nf-core/fcs/fcsgx | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/buildcustom | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/classify | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/report | ||
| - profile: conda | ||
| path: modules/nf-core/ganon/table | ||
| - profile: conda | ||
| path: modules/nf-core/gatk4/cnnscorevariants | ||
| - profile: conda | ||
| path: modules/nf-core/gatk4/determinegermlinecontigploidy | ||
| - profile: conda | ||
| path: modules/nf-core/genescopefk | ||
| - profile: conda | ||
| path: modules/nf-core/ilastik/multicut | ||
| - profile: conda | ||
| path: modules/nf-core/ilastik/pixelclassification | ||
| - profile: conda | ||
| path: modules/nf-core/imputeme/vcftoprs | ||
| - profile: conda | ||
| path: modules/nf-core/mcquant | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/katcomp | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/katgc | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/merquryfk | ||
| - profile: conda | ||
| path: modules/nf-core/merquryfk/ploidyplot | ||
| - profile: conda | ||
| path: modules/nf-core/molkartgarage/clahe | ||
| - profile: conda | ||
| path: modules/nf-core/quartonotebook | ||
| - profile: conda | ||
| path: modules/nf-core/scimap/spatiallda | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/bwaindex | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/bwamem | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/dedup | ||
| - profile: conda | ||
| path: modules/nf-core/sentieon/qualcal | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/mkgtf | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/mkref | ||
| - profile: conda | ||
| path: modules/nf-core/spaceranger/count | ||
| - profile: conda | ||
| path: modules/nf-core/spotiflow | ||
| - profile: conda | ||
| path: modules/nf-core/svanalyzer/svbenchmark | ||
| - profile: conda | ||
| path: modules/nf-core/universc | ||
| - profile: singularity | ||
| path: modules/nf-core/universc | ||
| - profile: conda | ||
| path: modules/nf-core/vt/decompose | ||
| - profile: singularity | ||
| path: modules/nf-core/bases2fastq | ||
| - profile: conda | ||
| path: modules/nf-core/wittyer | ||
| - profile: conda | ||
| path: modules/nf-core/islandpath | ||
| - profile: conda | ||
| path: subworkflows/nf-core/vcf_annotate_ensemblvep | ||
| - profile: conda | ||
| path: subworkflows/nf-core/bcl_demultiplex | ||
| - profile: conda | ||
| path: subworkflows/nf-core/fastq_align_bamcmp_bwa | ||
| - profile: conda | ||
| path: subworkflows/nf-core/fastq_align_bwa | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.9.0" | ||
| TOTAL_SHARDS: 3 | ||
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | ||
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | ||
| steps: | ||
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | ||
| - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # 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 | ||
| - 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@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | ||
| with: | ||
| python-version: "3.11" | ||
| - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # 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,defaults | ||
| - 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 Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) | ||
| 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 }} \ | ||
| --tap=test.tap \ | ||
| --ci \ | ||
| --verbose \ | ||
| --only-changed \ | ||
| --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ | ||
| --filter ${{ matrix.filter }} \ | ||
| --follow-dependencies | ||
| - name: | ||
| run: nf-test test --ci | ||
| - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | ||
| with: | ||
| path: >- | ||
| test.tap | ||
| - name: Clean up | ||
| if: always() | ||
| run: | | ||
| sudo rm -rf /home/ubuntu/tests/ | ||
