From 463bb3b0004a27aa02bcaf00a90fe8a06955256c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 14:07:00 +0200
Subject: [PATCH] ucsc: wig_to_bedgraph replace by an awk cmd
---
src/nf_modules/ucsc/main.nf | 12 +++---------
1 file changed, 3 insertions(+), 9 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 91469781..6eeefa83 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -53,9 +53,7 @@ process wig_to_bedgraph {
script:
"""
-wigToBigWig ${wig} ${wig.simpleName}.bw
-bigWigToBedGraph ${wig.simpleName}.bw ${wig.simpleName}.bg
-rm ${wig.simpleName}.bw
+awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig} > ${wig.simpleName}.bg
"""
}
@@ -77,12 +75,8 @@ process wig2_to_bedgraph2 {
script:
"""
-wigToBigWig ${wig_a} ${wig_a.simpleName}.bw
-bigWigToBedGraph ${wig_a.simpleName}.bw ${wig_a.simpleName}.bg
-rm ${wig_a.simpleName}.bw
-wigToBigWig ${wig_b} ${wig_b.simpleName}.bw
-bigWigToBedGraph ${wig_b.simpleName}.bw ${wig_b.simpleName}.bg
-rm ${wig_b.simpleName}.bw
+awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig_a} > ${wig_a.simpleName}.bg
+awk '{print \$1"\\t"\$2-1"\\t"\$2"\\t"\$3}' ${wig_b} > ${wig_b.simpleName}.bg
"""
}
--
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