From cc9b3a5020b749c5ce9301c54f2d0cc997622d28 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 14:06:37 +0200
Subject: [PATCH] ucsc: update bigwig2_to_wig2 to match changes in
bigwig_to_wig
---
src/nf_modules/ucsc/main.nf | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 899157f9..fefde335 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -74,11 +74,13 @@ process bigwig2_to_wig2 {
script:
"""
-bigWigToWig ${params.bigwig_to_wig} \
+bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_a} \
- ${bw_a.simpleName}.wig
-bigWigToWig ${params.bigwig_to_wig} \
+ ${bw_a.simpleName}.bg
+awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.bg > ${bw_a.simpleName}.wig
+bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_b} \
- ${bw_b.simpleName}.wig
+ ${bw_b.simpleName}.bg
+awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.bg > ${bw_b.simpleName}.wig
"""
}
\ No newline at end of file
--
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