Adding plot coverage option to run usage #31
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| name: tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Dry_Run_and_Lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:v5.24.2 | |
| - name: Dry Run with test data | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/mpox-seek run --input \ | |
| /opt2/.tests/WT_S1_0.fastq.gz /opt2/.tests/WT_S1_1.fastq.gz \ | |
| /opt2/.tests/WT_S2_0.fastq.gz /opt2/.tests/WT_S2_1.fastq.gz \ | |
| /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \ | |
| /opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \ | |
| /opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \ | |
| --output /opt2/output --mode local --dry-run | |
| - name: Dry Run with test data using all cli options | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/mpox-seek run --input \ | |
| /opt2/.tests/WT_S1_0.fastq.gz /opt2/.tests/WT_S1_1.fastq.gz \ | |
| /opt2/.tests/WT_S2_0.fastq.gz /opt2/.tests/WT_S2_1.fastq.gz \ | |
| /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \ | |
| /opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \ | |
| /opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \ | |
| --output /opt2/output --mode local --batch-id 2024-04-03 \ | |
| --additional-strains /opt2/resources/mpox_additional_strains.fa.gz \ | |
| --bootstrap-trees \ | |
| --dry-run | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/output/config.json | |
| - name: Lint Workflow | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' |