From 318780aa03e8c1cfbce0129137c2c6b7e0687f0c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 14:52:52 +0200
Subject: [PATCH] danpos: change dpeak output cardinality
---
src/nf_modules/danpos/main.nf | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 720988de..7814ec80 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -181,7 +181,8 @@ process dpeak_bam {
tuple val(file_id), path(bam_ip), path(bam_wce)
output:
- tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}.bgsub.wig"), path("${file_prefix}/${bam_wce.simpleName}.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.position.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
@@ -241,8 +242,8 @@ process dpeak_wig {
tuple val(file_id), path(wig_ip), path(wig_wce)
output:
- tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
- tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
+ tuple val(file_id), path("${file_prefix}/${wig_ip.simpleName}.bgsub.wig"), path("${file_prefix}/${wig_wce.simpleName}.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.position.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -272,7 +273,7 @@ danpos.py dpeak -m ${m} \
mv ${file_prefix}/pooled/* ${file_prefix}/
rm -R ${file_prefix}/pooled
awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.bed
-awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.summit.bed
+awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_wce.simpleName}.bgsub.peaks.xls > ${file_prefix}/${wig_ip.simpleName}.bgsub.positions.summit.bed
"""
}
--
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