From 019cbb96a68c2fca141c955126b0ad9b97511f2a Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 14 Dec 2021 16:00:30 +0100
Subject: [PATCH] More correct evaluation of controlBams input
---
macs2.wdl | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index 983630c..eb71ac1 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -24,8 +24,8 @@ task PeakCalling {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
- Array[File]+? controlBams
- Array[File]+? controlBamsIndex
+ Array[File] controlBams
+ Array[File] controlBamsIndex
String outDir = "macs2"
String sampleName
Boolean nomodel = false
@@ -38,7 +38,7 @@ task PeakCalling {
set -e
macs2 callpeak \
--treatment ~{sep = ' ' inputBams} \
- ~{true="--control" false="" defined(controlBams)} ~{sep = ' ' controlBams} \
+ ~{true="--control" false="" length(controlBams) > 0} ~{sep = ' ' controlBams} \
--outdir ~{outDir} \
--name ~{sampleName} \
~{true='--nomodel' false='' nomodel}
@@ -57,8 +57,8 @@ task PeakCalling {
parameter_meta {
inputBams: {description: "The BAM files on which to perform peak calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
- controlBams: {description: "Control BAM files for the input bam files.", category: "required"}
- controlBamsIndex: {description: "The indexes for the control BAM files.", category: "required"}
+ controlBams: {description: "Control BAM files for the input bam files.", category: "common"}
+ controlBamsIndex: {description: "The indexes for the control BAM files.", category: "common"}
sampleName: {description: "Name of the sample to be analysed", category: "required"}
outDir: {description: "All output files will be written in this directory.", category: "advanced"}
nomodel: {description: "Whether or not to build the shifting model.", category: "advanced"}
--
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