From b16d01fc04056fb54ac9bd91d68c5f5a58c56a95 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Feb 2021 08:57:01 +0100
Subject: [PATCH] nf_modules: add ucsc bg to bw sorting step
---
src/nf_modules/ucsc/main.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index c63de6e2..b4fe98df 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -18,7 +18,8 @@ process bedgraph_to_bigwig {
# transform bed file of start-stop chromosome size to stop chromosome size
awk -v OFS="\\t" '{print \$1, \$3}' ${bed} > chromsize.txt
-bedGraphToBigWig ${bg} \
+sort -T ./ -k1,1 -k2,2n ${bg} > \
+ bedGraphToBigWig - \
chromsize.txt \
${bg.simpleName}_norm.bw
"""
--
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