Merge pull request #538 from sofstam/bump_post_release #1878
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] | |
| 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 |