From 9db6166a54582bad47add39ac85e1701253cf069 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 09:44:15 +0200
Subject: [PATCH] danpos: add xls to bed convertion in every process
---
src/nf_modules/danpos/main.nf | 20 ++++++++++++++++++++
1 file changed, 20 insertions(+)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 3bcd4e6b..1e503b56 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -38,6 +38,7 @@ process dpos_bam {
output:
tuple val(file_id), path("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -64,6 +65,10 @@ danpos.py dpos -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
"""
}
@@ -92,6 +97,7 @@ process dpos_wig {
output:
tuple val(file_id), path("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
script:
@@ -118,6 +124,10 @@ danpos.py dpos -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, "+" }' ${file_prefix}/${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
"""
}
@@ -152,6 +162,7 @@ process dpos_wigvswig {
output:
tuple val(file_id), path("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id_a), path("${file_prefix}"), emit: folder
script:
@@ -178,6 +189,10 @@ danpos.py dpos -m ${m} \
-b ${wig_ip_a}:${wig_wce_a},${wig_ip_b}:${wig_wce_b} \
-o ${file_prefix} \
${wig_ip_a}:${wig_ip_b}
+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
"""
}
@@ -325,6 +340,7 @@ process dpeak_wigvswig {
output:
tuple val(file_id_a), path("${file_prefix}/pooled/*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id_a), path("${file_prefix}"), emit: folder
script:
@@ -351,5 +367,9 @@ danpos.py dpeak -m ${m} \
-b ${wig_ip_a}:${wig_wce_a},${wig_ip_b}:${wig_wce_b} \
-o ${file_prefix} \
${wig_ip_a}:${wig_ip_b}
+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
"""
}
\ No newline at end of file
--
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