From 34b3732319f7d74c72f93ff1bcb05ccc675585f8 Mon Sep 17 00:00:00 2001
From: imoustakas <i.moustakas@lumc.nl>
Date: Wed, 25 Jan 2023 16:47:10 +0100
Subject: [PATCH] Add a number of macs2 flags so we can adhere to Encode
---
macs2.wdl | 25 +++++++++++++++++++++++--
1 file changed, 23 insertions(+), 2 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index e6a011a..53be0ab 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -30,8 +30,15 @@ task PeakCalling {
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"
+ String callsummits = true
Int timeMinutes = 600 # Default to 10 hours
- String memory = "8GiB"
+ String memory = "8G"
String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
}
@@ -43,7 +50,14 @@ task PeakCalling {
--outdir ~{outDir} \
--name ~{sampleName} \
-f ~{format} \
- ~{true='--nomodel' false='' nomodel}
+ -g ~{gensz} \
+ -p ~{pval_thres} \
+ --shift ~{shiftsize} \
+ --extsize ~{extsize} \
+ ~{true='--nomodel' false='' nomodel} \
+ ~{true='-B' false='' bdg} \
+ --keep-dup ~{keepdup} \
+ ~{true='--call-summits' false='' callsummits}
}
output {
@@ -64,6 +78,13 @@ task PeakCalling {
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"}
+ gensz: {description: "macs2 argument for setting the mappable genome size or effective genome size which is defined as the genome size which can be sequenced."}
+ pval_thres: {description: "macs2 argument for setting the p-value cutoff. If -p is specified, MACS2 will use p-value instead of q-value."}
+ shiftsize: {description: "macs2 argument to set an arbitrary shift in bp. Can be negative to indicate direction"}
+ extsize: {description: "macs2 argument to extend reads in 5'->3' direction to fix-sized fragments."}
+ bdg: {description: "macs2 argument that ebanbles the storage of the fragment pileup, control lambda in bedGraph files."}
+ keepdup: {description: "macs2 argument that controls the behavior towards duplicate tags at the exact same location."}
+ callsummits: {description: "macs2 argument to reanalyze the shape of signal profile to deconvolve subpeaks within each peak called from the general procedure."}
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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