From 719ddc7d4bbde0739cd7bb19a430eb67dc220e65 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 12:29:14 +0200
Subject: [PATCH] ucsc: fix wig_to_bedgraph processes
---
src/nf_modules/ucsc/main.nf | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index ff3fbe27..91469781 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -53,7 +53,9 @@ process wig_to_bedgraph {
script:
"""
-wigToBedGraph ${wig} ${wig.simpleName}.bg
+wigToBigWig ${wig} ${wig.simpleName}.bw
+bigWigToBedGraph ${wig.simpleName}.bw ${wig.simpleName}.bg
+rm ${wig.simpleName}.bw
"""
}
@@ -75,8 +77,12 @@ process wig2_to_bedgraph2 {
script:
"""
-wigToBedGraph ${wig_a} ${wig_a.simpleName}.bg
-wigToBedGraph ${wig_b} ${wig_b.simpleName}.bg
+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
"""
}
--
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