Deploy dev branch to crazy-corgi #1988
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: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| test_name: | |
| - "test" | |
| - "test_nopreprocessing" | |
| - "test_noprofiling" | |
| - "test_krakenuniq" | |
| - "test_malt" | |
| - "test_motus" | |
| - "test_falco" | |
| - "test_fastp" | |
| - "test_alternativepreprocessing" | |
| - "test_bbduk" | |
| - "test_prinseqplusplus" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up 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 | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| conda-solver: libmamba | |
| channels: conda-forge,bioconda | |
| - name: Set up Conda | |
| if: matrix.profile == 'conda' | |
| run: | | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| if [[ "${{ matrix.test_name }}" == "test_motus" ]]; then | |
| wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py | |
| python downloadDB.py --no-download-progress | |
| echo 'tool,db_name,db_params,db_type,db_path' > 'database_motus.csv' | |
| echo "motus,db1_mOTU,,short,db_mOTU" >> 'database_motus.csv' | |
| echo "motus,db2_mOTU,,long,db_mOTU" >> 'database_motus.csv' | |
| echo "motus,db3_mOTU,,short;long,db_mOTU" >> 'database_motus.csv' | |
| nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.test_name }} --databases ./database_motus.csv --outdir ./results_${{ matrix.test_name }}; | |
| else | |
| nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.test_name }} --outdir ./results_${{ matrix.test_name }}; | |
| fi |