add threads to bamCoverage

config/config.yaml

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

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}
         """