diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index b380d0d..1d0b06b 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -32,3 +32,23 @@ jobs: 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.' +Dry_Run_and_Lint_cellranger: + 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/cell-seek run --input \ + /opt2/.tests/WT/ \ + --output /opt2/output --genome hg38 --pipeline gex --cellranger 8.0.0 --mode local --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.' + diff --git a/.tests/WT/outs/web_summary.html b/.tests/WT/outs/web_summary.html new file mode 100644 index 0000000..e69de29