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}
         """
 
 
-- 
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