From 2dca5f3611fd3aef0ee501cbe05467b590c93280 Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Wed, 25 Jan 2023 17:29:04 +0100
Subject: [PATCH] Address comments from Ruben
---
macs2.wdl | 30 +++++++++++++++---------------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index 854db81..7b11c99 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -29,16 +29,16 @@ task PeakCalling {
String outDir = "macs2"
String sampleName
String format = "AUTO"
- Boolean nomodel = false
- String gensz = "hs"
- Int extsize
- Int shiftsize = -1*round(extsize/2)
- Float pval_thres = 0.01
- Boolean bdg = true
- String keepdup = "auto"
- Boolean callsummits = true
+ Boolean? nomodel
+ String? gensz
+ Int? extsize
+ Int? shiftsize = -1*round(extsize/2)
+ Float? pval_thres
+ Boolean? bdg
+ String? keepdup
+ Boolean? callsummits
Int timeMinutes = 600 # Default to 10 hours
- String memory = "8G"
+ String memory = "8GiB"
String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
}
@@ -49,14 +49,14 @@ task PeakCalling {
~{true="--control" false="" length(controlBams) > 0} ~{sep = ' ' controlBams} \
--outdir ~{outDir} \
--name ~{sampleName} \
- -f ~{format} \
- -g ~{gensz} \
- -p ~{pval_thres} \
- --shift ~{shiftsize} \
- --extsize ~{extsize} \
+ ~{"-f" + format} \
+ ~{"-g" + gensz} \
+ ~{"-p" + pval_thres} \
+ ~{"--shift" + shiftsize} \
+ ~{"--extsize" + extsize} \
~{true='--nomodel' false='' nomodel} \
~{true='-B' false='' bdg} \
- --keep-dup ~{keepdup} \
+ ~{"--keep-dup" + keepdup} \
~{true='--call-summits' false='' callsummits}
}
--
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