update blacklist beds, archive, add docs for new lists, change paths … #4
Workflow file for this run
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| name: DevTesting | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| jobs: | |
| deploy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: docker://snakemake/snakemake:v7.19.1 | |
| with: | |
| directory: '.test' | |
| snakefile: 'workflow/Snakefile' | |
| args: '--cores 1 --use-conda --conda-cleanup-pkgs cache' | |
| stagein: '' # additional preliminary commands to run (can be multiline) | |
| - name: Dev Testing 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.'" |