Bin QC Improvements #1886
Workflow file for this run
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/mag') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| test_name: | |
| - "test" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # 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 ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results | |
| profiles: | |
| name: Run workflow profile | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Run remaining test profiles with minimum nextflow version | |
| test_name: | |
| [ | |
| test_host_rm, | |
| test_hybrid, | |
| test_hybrid_host_rm, | |
| test_busco_auto, | |
| test_ancient_dna, | |
| test_adapterremoval, | |
| test_binrefinement, | |
| test_virus_identification, | |
| test_single_end, | |
| test_concoct, | |
| ] | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with ${{ matrix.test_name }} test profile | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},docker --outdir ./results | |
| checkm: | |
| name: Run single test to checkm due to database download | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Download and prepare CheckM database | |
| run: | | |
| mkdir -p databases/checkm | |
| wget https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz -P databases/checkm | |
| tar xzvf databases/checkm/checkm_data_2015_01_16.tar.gz -C databases/checkm/ | |
| - name: Run pipeline with ${{ matrix.profile }} test profile | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm | |
| checkm2: | |
| name: Run single test to checkm2 due to database download | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Download and prepare CheckM2 database | |
| run: | | |
| mkdir -p databases/checkm2 | |
| wget https://zenodo.org/records/5571251/files/checkm2_database.tar.gz -P databases/checkm2 | |
| tar xzvf databases/checkm2/checkm2_database.tar.gz -C databases/checkm2/ | |
| - name: Run pipeline with ${{ matrix.profile }} test profile | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} \ | |
| -profile test,docker \ | |
| --outdir ./results \ | |
| --binqc_tool checkm2 \ | |
| --checkm2_db databases/checkm2/CheckM2_database/uniref100.KO.1.dmnd |