From b0f22ec204c9f4097a67106e7178cc08bb83648a Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 10 Feb 2021 08:53:02 +0100
Subject: [PATCH] nf_modules: add ucsc bg to bw
---
src/nf_modules/ucsc/main.nf | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
create mode 100644 src/nf_modules/ucsc/main.nf
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
new file mode 100644
index 00000000..c63de6e2
--- /dev/null
+++ b/src/nf_modules/ucsc/main.nf
@@ -0,0 +1,26 @@
+version = "407"
+container_url = "lbmc/ucsc:${version}"
+
+process bedgraph_to_bigwig {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${file_id}"
+
+ input:
+ tuple val(file_id) path(bg)
+ tuple val(file_id) path(bed)
+
+ output:
+ tuple val(file_id), path("*.bw"), emit: fasta
+
+ script:
+"""
+# transform bed file of start-stop chromosome size to stop chromosome size
+awk -v OFS="\\t" '{print \$1, \$3}' ${bed} > chromsize.txt
+
+bedGraphToBigWig ${bg} \
+ chromsize.txt \
+ ${bg.simpleName}_norm.bw
+"""
+}
+
--
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