Adding json module from stdlib #62
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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, all options | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/cyte-seek run --genome hg38 --input \ | |
| /opt2/.tests/1_HTO1_S1_R1_001.fastq.gz /opt2/.tests/1_HTO1_S1_R2_001.fastq.gz \ | |
| /opt2/.tests/2_HTO2_S2_R1_001.fastq.gz /opt2/.tests/2_HTO2_S2_R2_001.fastq.gz \ | |
| /opt2/.tests/3_ADT1_S1_R1_001.fastq.gz /opt2/.tests/3_ADT1_S1_R2_001.fastq.gz \ | |
| /opt2/.tests/4_ADT2_S2_R1_001.fastq.gz /opt2/.tests/4_ADT2_S2_R2_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L001_I1_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L001_R2_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L002_R1_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L002_R2_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L001_I1_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L001_R2_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L002_R1_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L002_R2_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L001_I1_001.fastq.gz /opt2/.tests/Undetermined_S0_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L001_R2_001.fastq.gz /opt2/.tests/Undetermined_S0_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L002_R1_001.fastq.gz /opt2/.tests/Undetermined_S0_L002_R2_001.fastq.gz \ | |
| --libraries /opt2/.tests/libraries.csv --features /opt2/.tests/features.csv \ | |
| --num-cells 4000 --force-cells --pre-mrna --output /opt2/output --mode local --dry-run | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/output/config.json | |
| - name: Dry Run with test data, use defaults | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/cyte-seek run --genome hg38 --input \ | |
| /opt2/.tests/1_HTO1_S1_R1_001.fastq.gz /opt2/.tests/1_HTO1_S1_R2_001.fastq.gz \ | |
| /opt2/.tests/2_HTO2_S2_R1_001.fastq.gz /opt2/.tests/2_HTO2_S2_R2_001.fastq.gz \ | |
| /opt2/.tests/3_ADT1_S1_R1_001.fastq.gz /opt2/.tests/3_ADT1_S1_R2_001.fastq.gz \ | |
| /opt2/.tests/4_ADT2_S2_R1_001.fastq.gz /opt2/.tests/4_ADT2_S2_R2_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L001_I1_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L001_R2_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/5_cDNA1_S1_L002_R1_001.fastq.gz /opt2/.tests/5_cDNA1_S1_L002_R2_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L001_I1_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L001_R2_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/6_cDNA2_S2_L002_R1_001.fastq.gz /opt2/.tests/6_cDNA2_S2_L002_R2_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L001_I1_001.fastq.gz /opt2/.tests/Undetermined_S0_L001_R1_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L001_R2_001.fastq.gz /opt2/.tests/Undetermined_S0_L002_I1_001.fastq.gz \ | |
| /opt2/.tests/Undetermined_S0_L002_R1_001.fastq.gz /opt2/.tests/Undetermined_S0_L002_R2_001.fastq.gz \ | |
| --libraries /opt2/.tests/libraries.csv --features /opt2/.tests/features.csv \ | |
| --output /opt2/output --mode local --dry-run | |
| - 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.' |