From a2c7c8e54c862382131b5401ddb7adf04ecfabe3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 10:44:29 +0200
Subject: [PATCH] danpos: rm position.summit not present for dpos
---
src/nf_modules/danpos/main.nf | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index a17e2ca1..174c4cfd 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -40,7 +40,7 @@ process dpos_bam {
output:
tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), emit: wig
- tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -69,7 +69,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
-awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed
"""
}
@@ -102,7 +101,7 @@ process dpos_wig {
output:
tuple val(file_id), path("${file_prefix}/${wig_ip.simpleName}*.wig"), emit: wig
- tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -131,7 +130,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
-awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed
"""
}
@@ -170,7 +168,7 @@ process dpos_wigvswig {
output:
tuple val(file_id), path("${file_prefix}/${wig_ip_a.simpleName}*.wig"), emit: wig
- tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
tuple val(file_id_a), path("${file_prefix}"), emit: folder
script:
@@ -200,7 +198,6 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
-awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$4-1, \$4, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.peaks.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.summit.bed
"""
}
--
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