From 59ad480a0704ab4e37ada170fbb6cee4b4bcbee8 Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Mon, 24 Sep 2018 13:40:00 +0200
Subject: [PATCH] Add control sample functionality
---
macs2.wdl | 3 +++
1 file changed, 3 insertions(+)
diff --git a/macs2.wdl b/macs2.wdl
index 982802f..fd2dd6f 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -7,6 +7,8 @@ task PeakCalling {
String? preCommand
Array[File]+ inputBams
Array[File]+ inputBamsIndex
+ Array[File]? controlBams
+ Array[File]? controlBamsIndex
String outDir
String sampleName
Int threads = 1
@@ -19,6 +21,7 @@ task PeakCalling {
~{preCommand}
macs2 callpeak \
--treatment ~{sep = ' ' inputBams} \
+ ~{true="--control" false="" defined(controlBams)} ~{sep = ' ' controlBams} \
--outdir ~{outDir} \
--name ~{sampleName} \
~{true='--nomodel' false='' nomodel}
--
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