diff --git a/config/config.yaml b/config/config.yaml index 2c920de03b30a762588fbbeb9389f7d607aa80c8..86e8f3f451fb48b06db7dab6dae2c7e79e8fe780 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -168,7 +168,7 @@ feature_counts: bamCoverage: do: yes options: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 --normalizeUsing RPKM" - + threads: 4 #=============================================================================== diff --git a/workflow/rules/bamCoverage.rules b/workflow/rules/bamCoverage.rules index 7c6167f91010f1056febf3c59d1abe73a8a42d35..535b8d577180782dec0668dcff16dca03dfad558 100755 --- a/workflow/rules/bamCoverage.rules +++ b/workflow/rules/bamCoverage.rules @@ -36,9 +36,11 @@ rule bamCoverage: options = bamCoverage_options envmodules: "deepTools" + threads: + config['bamCoverage']['threads'] shell: """ - bamCoverage --bam {input} --outFileName {output} {params.options} 2> {log} + bamCoverage --bam {input} --outFileName {output} {params.options} --numberOfProcessors {threads} 2> {log} """