From bd7dec8fd69f8004f55f30e6e6a20a970189ac0e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 10:15:28 +0100
Subject: [PATCH] macs3: test new syntax for options
---
src/nf_modules/macs3/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/macs3/main.nf b/src/nf_modules/macs3/main.nf
index bc32f4e9..4dcc9cd4 100644
--- a/src/nf_modules/macs3/main.nf
+++ b/src/nf_modules/macs3/main.nf
@@ -20,9 +20,9 @@ process peak_calling {
"""
macs3 callpeak \
--treatment ${bam_ip} \
- --call-summits "True"\
+ --call-summits True \
--control ${bam_control} \
- --keep-dup "auto" \
+ --keep-dup all \
--name ${bam_ip.simpleName} \
--gsize ${macs3_genome_size} 2> \
${bam_ip.simpleName}_macs3_report.txt
@@ -55,9 +55,9 @@ awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${bg_control} > \
${bg_control.simpleName}.bed
macs3 callpeak \
--treatment ${bg_ip.simpleName}.bed \
- --call-summits "True"\
+ --call-summits True \
--control ${bg_control.simpleName}.bed \
- --keep-dup "auto" \
+ --keep-dup all \
--name ${bg_ip.simpleName} \
--gsize ${macs3_genome_size} 2> \
${bg_ip.simpleName}_macs3_report.txt
--
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