Add support for presupplied annotation files (FAA + GFF or FAA + GBK) #1152
Workflow file for this run
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| 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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data (AMP/ARG) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| parameters: | |
| - "-profile docker,test_preannotated --annotation_tool prodigal" | |
| - "-profile docker,test --annotation_tool prokka" | |
| - "-profile docker,test --annotation_tool bakta --annotation_bakta_db_downloadtype light --arg_skip_deeparg --arg_skip_amrfinderplus" # Skip deeparg and amrfinderplus due to otherwise running out of space on GitHub Actions | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data (AMP and ARG workflows) | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} ${{ matrix.parameters }} --outdir ./results | |
| test_bgc: | |
| name: Run pipeline with test data (BGC) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| parameters: | |
| - "-profile docker,test_preannotated_bgc --annotation_tool prodigal" | |
| - "-profile docker,test_bgc --annotation_tool prokka" | |
| - "-profile docker,test_bgc --annotation_tool bakta --annotation_bakta_db_downloadtype light" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data (BGC workflow) | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} ${{ matrix.parameters }} --outdir ./results --bgc_skip_deepbgc | |
| test_taxonomy: | |
| name: Run pipeline with test data (AMP, ARG and BGC taxonomy) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| parameters: | |
| - "-profile docker,test_taxonomy --annotation_tool prodigal" # TODO: Add test_taxonomy_preannotated.config | |
| - "-profile docker,test_taxonomy --annotation_tool prokka" | |
| - "-profile docker,test_taxonomy --annotation_tool bakta --annotation_bakta_db_downloadtype light" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data (AMP, ARG and BGC taxonomy workflows) | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} ${{ matrix.parameters }} --outdir ./results |