From 561414d26fadd830a54c3a680a56f26133bd1051 Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Mon, 23 Jul 2018 13:51:01 +0200
Subject: [PATCH] Fix output directory
---
macs2.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index 612e5d1..1a02d77 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -12,13 +12,13 @@ task PeakCalling {
${preCommand}
macs2 callpeak \
--treatment ${sep = ' ' bamFiles} \
- --outdir ${outDir} \
+ --outdir ${outDir} + "/macs2/" \
--name ${sampleName} \
${true='--nomodel' false='' nomodel}
}
output {
- File peakFile = outDir + "/" + sampleName + "/macs2/" + sampleName + "_peaks.narrowPeak"
+ File peakFile = outDir + "/macs2/" + sampleName + "_peaks.narrowPeak"
}
runtime {
--
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