Ensure alternative long-read processing tools included in tests #1820
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 | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| tags: | |
| - "test" | |
| - "test_nopreprocessing" | |
| - "test_noprofiling" | |
| - "test_krakenuniq" | |
| - "test_malt" | |
| - "test_motus" | |
| - "test_falco" | |
| - "test_fastp" | |
| - "test_alternativepreprocessing" | |
| - "test_bbduk" | |
| - "test_prinseqplusplus" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| sudo locale-gen en_US.UTF-8 | |
| sudo update-locale LANG=en_US.UTF-8 | |
| - name: Run pipeline with test data | |
| run: | | |
| if [[ "${{ matrix.tags }}" == "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.tags }} --databases ./database_motus.csv --outdir ./results_${{ matrix.tags }}; | |
| else | |
| nextflow run ${GITHUB_WORKSPACE} -profile docker,${{ matrix.tags }} --outdir ./results_${{ matrix.tags }}; | |
| fi |