From 9021172a1bb5125c996d303555b884214d026952 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 10:48:10 +0200
Subject: [PATCH] danpos: replace peaks by positions for dpos outputs
---
src/nf_modules/danpos/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 174c4cfd..a2e7861a 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -68,7 +68,7 @@ danpos.py dpos -m ${m} \
${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, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
"""
}
@@ -129,7 +129,7 @@ danpos.py dpos -m ${m} \
${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, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
"""
}
@@ -197,7 +197,7 @@ danpos.py dpos -m ${m} \
${wig_ip_a}:${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, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.xls > ${file_prefix}/${bam_ip.simpleName}.bgsub.positions.bed
"""
}
--
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