From 5df62f54b036d396ad78c966e19956a47df552c3 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 14 Jan 2022 13:49:16 +0100
Subject: [PATCH] Add format parameter to macs2

---
 macs2.wdl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/macs2.wdl b/macs2.wdl
index eb71ac1..e17d613 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -28,6 +28,7 @@ task PeakCalling {
         Array[File] controlBamsIndex
         String outDir = "macs2"
         String sampleName
+        String format = "AUTO"
         Boolean nomodel = false
         Int timeMinutes = 600  # Default to 10 hours
         String memory = "8G"
@@ -41,6 +42,7 @@ task PeakCalling {
         ~{true="--control" false="" length(controlBams) > 0} ~{sep = ' ' controlBams} \
         --outdir ~{outDir} \
         --name ~{sampleName} \
+        -f ~{format} \
         ~{true='--nomodel' false='' nomodel}
     }
 
-- 
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