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fix: scratch path update, log file dir update #46

fix: scratch path update, log file dir update

fix: scratch path update, log file dir update #46

Workflow file for this run

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.'"