From 3b38b233ab4521ae0ede5cca8d64d9ce790832f5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 13:58:53 +0200
Subject: [PATCH] ucsc: improve bigwig_to_wig
---
src/nf_modules/ucsc/main.nf | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 323536a0..28967df5 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -49,9 +49,10 @@ process bigwig_to_wig {
script:
"""
-bigWigToWig ${params.bigwig_to_wig} \
+bigWigToBedGraph ${params.bigwig_to_wig} \
${bg} \
- ${bg.simpleName}.wig
+ ${bg.simpleName}.bg
+awk '{if(NR>1) {if($1!=lastChrom){printf("variableStep chrom=%s\n",$1);lastChrom=$1;}print $2,$4}}' ${bg.simpleName}.bg > ${bg.simpleName}.wig
"""
}
--
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