make a variety of improvements to the summary plots #271
Workflow file for this run
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| name: Run tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: build conda environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: dms-vep-pipeline-3 | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| auto-update-conda: true | |
| channel-priority: strict | |
| - name: lint with ruff | |
| # NOTE: must specify the shell so that conda init updates bashrc see: | |
| # https://github.com/conda-incubator/setup-miniconda#IMPORTANT | |
| shell: bash -el {0} | |
| run: ruff check . | |
| - name: check code format with black | |
| shell: bash -el {0} | |
| run: black --check . | |
| - name: check snakemake files format with snakefmt | |
| shell: bash -el {0} | |
| run: snakefmt --check . | |
| - name: lint snakemake files with snakemake --lint | |
| shell: bash -el {0} | |
| run: cd test_example && snakemake -s ../Snakefile --lint && cd .. | |
| - name: run pipeline with default config | |
| shell: bash -el {0} | |
| run: > | |
| rm -rf docs | |
| && cd test_example | |
| && rm -rf results | |
| && snakemake -s ../Snakefile -j 2 | |
| && cd .. | |
| - name: compare results to expected | |
| shell: bash -el {0} | |
| run: > | |
| cd test_example | |
| && python compare_results_to_expected.py | |
| && cd .. | |
| - name: run pipeline with prebuilt variants and counts | |
| shell: bash -el {0} | |
| run: > | |
| rm -rf docs | |
| && cd test_example | |
| && cd results | |
| && rm -rf antibody_escape func_effect_diffs func_effect_shifts summaries func_effects func_scores receptor_affinity | |
| && cd .. | |
| && rm -rf sequencing_data | |
| && snakemake -s ../Snakefile -j 2 --config prebuilt_variants=https://raw.githubusercontent.com/dms-vep/dms-vep-pipeline-3/main/test_example/results/variants/codon_variants.csv prebuilt_geneseq=https://raw.githubusercontent.com/dms-vep/dms-vep-pipeline-3/main/test_example/results/gene_sequence/codon.fasta use_precomputed_barcode_counts=true | |
| && cd .. | |
| - name: Upload log files in case of error | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: log-files | |
| path: test_example/results/logs | |
| retention-days: 7 |