From 8d12bcf2177948c6f7dbfef90966b684cd43dc74 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 09:56:45 +0100
Subject: [PATCH] macs3: fix file names
---
src/nf_modules/macs3/main.nf | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/src/nf_modules/macs3/main.nf b/src/nf_modules/macs3/main.nf
index 8995b2d6..4b8aa78e 100644
--- a/src/nf_modules/macs3/main.nf
+++ b/src/nf_modules/macs3/main.nf
@@ -17,9 +17,9 @@ process peak_calling {
/* remove --nomodel option for real dataset */
"""
macs2 callpeak \
- --treatment ${file_ip} \
+ --treatment ${bam_ip} \
--call-summits "True"\
- --control ${file_control} \
+ --control ${bam_control} \
--keep-dup "auto" \
--name ${bam_ip.simpleName} \
--gsize ${macs3_genome_size} 2> \
@@ -47,20 +47,20 @@ process peak_calling_bg {
script:
/* remove --nomodel option for real dataset */
"""
-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} > \
- ${file_control.simpleName}.bed
+awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${bg_ip} > \
+ ${bg_ip.simpleName}.bed
+awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${bg_control} > \
+ ${bg_control.simpleName}.bed
macs2 callpeak \
- --treatment ${file_ip.simpleName}.bed \
+ --treatment ${bg_ip.simpleName}.bed \
--call-summits "True"\
- --control ${file_control.simpleName}.bed \
+ --control ${bg_control.simpleName}.bed \
--keep-dup "auto" \
- --name ${bam_ip.simpleName} \
+ --name ${bg_ip.simpleName} \
--gsize ${macs3_genome_size} 2> \
- ${bam_ip.simpleName}_macs3_report.txt
+ ${bg_ip.simpleName}_macs3_report.txt
-if grep -q "ERROR" ${bam_ip.simpleName}_macs3_report.txt; then
+if grep -q "ERROR" ${bg_ip.simpleName}_macs3_report.txt; then
echo "MACS3 error"
exit 1
fi
--
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