Provide the whole path #77
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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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| tags: | ||
| - "test" | ||
| - "test_nopreprocessing" | ||
| - "test_noprofiling" | ||
| - "test_krakenuniq" | ||
| - "test_malt" | ||
| - "test_motus" | ||
| - "test_falco" | ||
| - "test_fastp" | ||
| - "test_adapterremoval" | ||
| - "test_bbduk" | ||
| - "test_prinseqplusplus" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ 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: 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 > download_db_log.txt | ||
| echo 'tool,db_name,db_params,db_path' > 'database_motus.csv' | ||
| echo 'motus,db_mOTU,,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_${{ matrix.tags }}; | ||
| fi | ||
| - name: Gather failed logs | ||
| if: failure() || cancelled() | ||
| run: | | ||
| mkdir failed_logs | ||
| failed=$(grep "FAILED" results/pipeline_info/execution_trace.txt | cut -f 2) | ||
| while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed" | ||
| - uses: actions/upload-artifact@v4 | ||
| if: failure() || cancelled() | ||
| name: Upload failed logs | ||
| with: | ||
| name: failed_logs | ||
| path: failed_logs | ||
| - uses: actions/upload-artifact@v4 | ||
| if: failure() | ||
| name: Upload work dir | ||
| path: /home/runner/work/taxprofiler/taxprofiler/work/ | ||
