fix: natural name sort bams #122
Workflow file for this run
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| name: Dry Runs | |
| on: | |
| push: | |
| jobs: | |
| dry_run_paired_end: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: 'true' | |
| - uses: docker://snakemake/snakemake:stable | |
| - name: Dry Run with test data | |
| run: | | |
| docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \ | |
| "source get_submods.sh; pip install -r requirements.txt; ./weave run --sheetname paired_end.csv -s /opt2/.tests/paired_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/paired_end" | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/.tests/dry_run_out/paired_end/.config/config_job_0.json | |
| - name: Lint Snakefile | |
| continue-on-error: true | |
| run: | | |
| docker run -e SNK_CONFIG='/opt2/.tests/dry_run_out/paired_end/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/Snakefile -d /opt2/workflow || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' | |
| dry_run_single_end: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: 'true' | |
| - uses: docker://snakemake/snakemake:stable | |
| - name: Dry Run with test data | |
| run: | | |
| docker run -h cn0000 -v $PWD:/opt2 -w /opt2 snakemake/snakemake:stable /bin/bash -c \ | |
| "source get_submods.sh; pip install -r requirements.txt;./weave run --sheetname single_end.csv -s /opt2/.tests/single_end -o /opt2/.tests/dry_run_out --local --dry-run /opt2/.tests/single_end" | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/.tests/dry_run_out/single_end/.config/config_job_0.json | |
| - name: Lint Snakefile | |
| continue-on-error: true | |
| run: | | |
| docker run -e SNK_CONFIG='/opt2/.tests/dry_run_out/single_end/.config/config_job_0.json' -v $PWD:/opt2 snakemake/snakemake:stable snakemake --lint -s /opt2/workflow/Snakefile -d /opt2/workflow || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' |