From eab763e83940670e35069bbbcbd22296ed7faef2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 09:53:28 +0100
Subject: [PATCH] macs3: fix awk cmd
---
src/nf_modules/macs3/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/macs3/main.nf b/src/nf_modules/macs3/main.nf
index b5b14056..8995b2d6 100644
--- a/src/nf_modules/macs3/main.nf
+++ b/src/nf_modules/macs3/main.nf
@@ -47,9 +47,9 @@ process peak_calling_bg {
script:
/* remove --nomodel option for real dataset */
"""
-awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_ip} > \
+awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${file_ip} > \
${file_ip.simpleName}.bed
-awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_control} > \
+awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${file_control} > \
${file_control.simpleName}.bed
macs2 callpeak \
--treatment ${file_ip.simpleName}.bed \
--
GitLab