bcftbx/mock: fix bug in 'MockIlluminaRun' when generating mock NovaSeq runs #154
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python CI | |
| on: [ push, pull_request ] | |
| jobs: | |
| build: | |
| # Switched from ubuntu-latest to ubuntu-20.04 as former | |
| # doesn't support Python 3.6 | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ['3.6', '3.7', '3.8', '3.9', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test bcftbx | |
| run: | | |
| python -m pip install . | |
| pytest bcftbx | |
| - name: Test illumina2cluster utilities | |
| run: | | |
| ./bin/prep_sample_sheet.py -h | |
| ./bin/verify_paired.py -h | |
| - name: Test solid2cluster utilities | |
| run: | | |
| ./bin/analyse_solid_run.py -h | |
| - name: Test RNA-seq utilities | |
| run: | | |
| examples/RNA-seq/test_bowtie_mapping_stats.sh | |
| - name: Test ChIP-seq utilities | |
| run: | | |
| examples/ChIP-seq/test_make_macs_xls.sh | |
| examples/ChIP-seq/test_make_macs2_xls.sh | |
| - name: Test NGS-general utilities | |
| run: | | |
| examples/NGS-general/test_extract_reads.sh | |
| ./bin/manage_seqs.py -h | |
| ./bin/reorder_fasta.py -h | |
| ./bin/sam2soap.py -h | |
| ./bin/split_fastq.py -h | |
| ./bin/split_fasta.py -h | |
| - name: Test microarray utilities | |
| run: | | |
| examples/microarray/test_annotate_probesets.sh | |
| examples/microarray/test_best_exons.sh | |
| examples/microarray/test_xrorthologs.sh | |
| - name: Test md5checker utility | |
| run: | | |
| examples/utils/test_md5checker.sh |