From 63746b007192626bfc2e47ae714050fba4873abf Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Mon, 2 Jul 2018 16:17:32 +0200
Subject: [PATCH] MACS2 takes array of files as input
---
macs2.wdl | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index 999f3f0..27775be 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -1,6 +1,6 @@
task peakCalling {
String? preCommand
- File bamFile
+ Array[File] bamFiles
String outDir
String sampleName
Int? threads
@@ -10,7 +10,10 @@ task peakCalling {
command {
set -e -o pipefail
${preCommand}
- macs2 callpeaks --treatment ${bamFile} --outdir ${outDir} --name ${sampleName}
+ macs2 callpeaks \
+ --treatment ${sep = ' ' bamFiles} \
+ --outdir ${outDir} \
+ --name ${sampleName}
}
output {
--
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