From 7b8843d446686843d80b0d66265e4054186a2c6b Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Thu, 28 Jun 2018 16:44:42 +0200
Subject: [PATCH] Add basic peakcalling with MACS2
---
macs2.wdl | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 macs2.wdl
diff --git a/macs2.wdl b/macs2.wdl
new file mode 100644
index 0000000..999f3f0
--- /dev/null
+++ b/macs2.wdl
@@ -0,0 +1,24 @@
+task peakCalling {
+ String? preCommand
+ File bamFile
+ String outDir
+ String sampleName
+ Int? threads
+ Int? memory
+
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ macs2 callpeaks --treatment ${bamFile} --outdir ${outDir} --name ${sampleName}
+ }
+
+ output {
+ File peakFile = outDir + "/" + sampleName + "/macs2/" + sampleName + "_peaks.narrowPeak"
+ }
+
+ runtime {
+ cpu: select_first([threads,1])
+ memory: select_first([memory,8])
+ }
+}
\ No newline at end of file
--
GitLab