From 4b9754f548b8558e7de2652e257edd807d0d4ffa Mon Sep 17 00:00:00 2001
From: Giannis Moustakas <johnmous@users.noreply.github.com>
Date: Thu, 26 Jan 2023 10:59:43 +0100
Subject: [PATCH] Update macs2.wdl
Co-authored-by: Davy Cats <davycats.dc@gmail.com>
---
macs2.wdl | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/macs2.wdl b/macs2.wdl
index c4c08ed..9d5344a 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -78,13 +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."}
+ 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.", category: "advanced"}
+ pval_thres: {description: "macs2 argument for setting the p-value cutoff. If -p is specified, MACS2 will use p-value instead of q-value.", category: "advanced"}
+ shiftsize: {description: "macs2 argument to set an arbitrary shift in bp. Can be negative to indicate direction.", category: "advanced"}
+ extsize: {description: "macs2 argument to extend reads in 5'->3' direction to fix-sized fragments.", category: "advanced"}
+ bdg: {description: "macs2 argument that enables the storage of the fragment pileup, control lambda in bedGraph files.", category: "advanced"}
+ keepdup: {description: "macs2 argument that controls the behavior towards duplicate tags at the exact same location.", category: "advanced"}
+ callsummits: {description: "macs2 argument to reanalyze the shape of signal profile to deconvolve subpeaks within each peak called from the general procedure.", 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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