Adding json module from stdlib #62
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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.' |