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Commit aa805acb authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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add threads to bamCoverage

parent a21c578b
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......@@ -168,7 +168,7 @@ feature_counts:
bamCoverage:
do: yes
options: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 --normalizeUsing RPKM"
threads: 4
#===============================================================================
......
......@@ -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}
"""
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