Create install script #58
Workflow file for this run
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name: lintr | |
on: | |
push: | |
branches: | |
- master | |
- dev | |
pull_request: | |
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.'" |