From a3e501f1e6a8c00d0d43b67461dc0e133020f111 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 23 Sep 2021 16:57:37 +0200
Subject: [PATCH] src/pipelines/nf_modules/peak_calling.nf: changes in
bedtools_slop and bedtools_merge
---
src/pipelines/nf_modules/peak_calling.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/pipelines/nf_modules/peak_calling.nf b/src/pipelines/nf_modules/peak_calling.nf
index 07f0b94..3e6645c 100644
--- a/src/pipelines/nf_modules/peak_calling.nf
+++ b/src/pipelines/nf_modules/peak_calling.nf
@@ -86,7 +86,7 @@ process bedtools_slop {
${new_id}.enlarged.tmp.bed
sort -k 1,1 -k2,2n ${new_id}.enlarged.tmp.bed > ${new_id}.enlarged.sort.bed
bedtools merge -i ${new_id}.enlarged.sort.bed \
- -d 6 -c 5,6 -o mean,distinct | awk '{print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$4"\\t"\$5}' > ${new_id}.merged.bed
+ -c 5,6 -o mean,distinct | awk '{print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$4"\\t"\$5}' > ${new_id}.merged.bed
"""
}
@@ -135,7 +135,7 @@ process bedtools_merge {
"""
cat *.bed | sort -k1,1 -k2,2n > tmp.bed
bedtools merge -i tmp.bed \
- -d 6 -c 1,5,6 -o count,mean,distinct | awk '{if(\$4 >= 2){print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$5"\\t"\$6}}' > ${sp}.rep_merged.bed
+ -c 1,5,6 -o count,mean,distinct | awk '{if(\$4 >= 2){print \$1"\\t"\$2"\\t"\$3"\\tpeak_"NR"\\t"\$5"\\t"\$6}}' > ${sp}.rep_merged.bed
"""
}
--
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