From c21d27ff32bdf7210dddf98a711e32192e820a82 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 14 Dec 2021 14:48:24 +0100
Subject: [PATCH] Add parameter_meta for macs2
---
macs2.wdl | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index 757eaf6..cbce18e 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -26,11 +26,10 @@ task PeakCalling {
Array[File]+ inputBamsIndex
Array[File]+? controlBams
Array[File]+? controlBamsIndex
- String outDir
+ String outDir = "macs2"
String sampleName
Boolean nomodel = false
- Int threads = 1
String memory = "8G"
String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
}
@@ -50,8 +49,21 @@ task PeakCalling {
}
runtime {
- cpu: threads
+ cpu: 1
memory: memory
docker: dockerImage
}
+ 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"}
+ 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"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+ }
}
--
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