Separate CI tests #1140
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] | ||
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| tags: | ||
| - "test" | ||
| - "test_full" | ||
| - "test_krakenuniq" | ||
| - "test_malt" | ||
| - "test_motus" | ||
| - "test_nopreprocessing" | ||
| - "test_noprofiling" | ||
| - "test_nothing" | ||
| parameters: | ||
| - "--preprocessing_qc_tool=falco" | ||
| - "--shortread_qc_tool=fastp" | ||
| - "--shortread_qc_tool=adapterremoval" | ||
| - "--shortread_complexityfilter_tool=bbduk" | ||
| - "--shortread_complexityfilter_tool=prinseqplusplus" | ||
| profile: | ||
| - "docker" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
| - name: Show current locale | ||
| run: locale | ||
| - name: Set UTF-8 enabled locale | ||
| run: | | ||
| sudo locale-gen en_US.UTF-8 | ||
| sudo update-locale LANG=en_US.UTF-8 | ||
| - name: Prepare the database for motus | ||
| if: matrix.tags == 'test_motus' | ||
| run: | | ||
| wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py | ||
| python downloadDB.py > download_db_log.txt | ||
| echo 'tool,db_name,db_params,db_path' > 'database_motus.csv' | ||
| echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv' | ||
| - name: Run pipeline with test data | ||
| uses: Wandalen/[email protected] | ||
| with: | ||
| command: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tags }},${{ matrix.profile }} ${{ matrix.parameters }} ${{ matrix.tags }} == 'test_motus' ? "--databases ./database_motus.csv" : "" --outdir ./results_${{ matrix.tags }} | ||
| attempt_limit: 3 | ||
