Fix CENTRIFUGE header modification when --out-fmt turned on #1096
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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| parameters: | |
| - "--preprocessing_qc_tool falco" | |
| - "--shortread_qc_tool fastp" | |
| - "--shortread_qc_tool adapterremoval" | |
| - "--shortread_complexityfilter_tool bbduk" | |
| - "--shortread_complexityfilter_tool prinseqplusplus" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ 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: Run pipeline with test data | |
| uses: Wandalen/[email protected] | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} | |
| attempt_limit: 3 | |
| motus: | |
| name: Test mOTUs with workflow parameters | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: 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 | |
| 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 test_motus,docker --outdir ./results --databases ./database_motus.csv | |
| attempt_limit: 3 | |
| krakenuniq: | |
| name: Test KrakenUniq with workflow parameters | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: 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 | |
| uses: Wandalen/[email protected] | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results | |
| attempt_limit: 3 | |
| malt: | |
| name: Test MALT with workflow parameters | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: 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 | |
| uses: Wandalen/[email protected] | |
| with: | |
| command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results | |
| attempt_limit: 3 |