fix: scratch path update, log file dir update #46
Workflow file for this run
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: lintr | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| jobs: | |
| Lintr: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:v7.19.1 | |
| - name: Lint Workflow | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v7.19.1 /bin/bash -c \ | |
| "mkdir -p /opt2/output_carlisle/config /opt2/output_carlisle/annotation && \ | |
| cp -r /opt2/workflow/scripts/ /opt2/output_carlisle/ && \ | |
| cp /opt2/resources/cluster_biowulf.yaml /opt2/output_carlisle/config/cluster.yaml && \ | |
| cp /opt2/resources/tools_biowulf.yaml /opt2/output_carlisle/config/tools.yaml && \ | |
| cd /opt2/output_carlisle/annotation && \ | |
| touch hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa && \ | |
| snakemake --lint -s /opt2/workflow/Snakefile \ | |
| -d /opt2/output_carlisle --configfile /opt2/.test/config_lint.yaml || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'" |