From d17e7d0031510588de5857a265f08686da639c5a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 14:45:13 +0200
Subject: [PATCH] danpos: add xls > bed convertion
---
src/nf_modules/danpos/main.nf | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 5946b856..720988de 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("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -208,6 +209,10 @@ danpos.py dpeak -m ${m} \
-b ${bam_wce} \
-o ${file_prefix} \
${bam_ip}
+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
"""
}
@@ -236,7 +241,8 @@ process dpeak_wig {
tuple val(file_id), path(wig_ip), path(wig_wce)
output:
- tuple val(file_id), path("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -263,6 +269,10 @@ danpos.py dpeak -m ${m} \
-b ${wig_wce} \
-o ${file_prefix} \
${wig_ip}
+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
"""
}
--
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