From aa805acb8c5f7adbcb688076a9a0b7f85c2d62e7 Mon Sep 17 00:00:00 2001 From: rlegendr <rachel.legendre@pasteur.fr> Date: Thu, 25 Feb 2021 15:11:23 +0100 Subject: [PATCH] add threads to bamCoverage --- config/config.yaml | 2 +- workflow/rules/bamCoverage.rules | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 2c920de..86e8f3f 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 7c6167f..535b8d5 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} """ -- GitLab