From 9aa94d395a1b975c8dc139280925b921154479a1 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 14 Oct 2021 16:28:22 +0200
Subject: [PATCH] ucsc: add wig_to_bedgraph
---
src/nf_modules/ucsc/main.nf | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index fbb166ef..6465cffc 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -35,6 +35,27 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \
"""
}
+params.wig_to_bedgraph = ""
+params.wig_to_bedgraph_out = ""
+process bigwig_to_wig {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${file_id}"
+ if (params.bigwig_to_wig_out != "") {
+ publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id) path(wig)
+
+ output:
+ tuple val(file_id), path("*.bg"), emit: wig
+
+ script:
+"""
+wigToBedGraph ${wig} ${wig.simpleName}.bg
+"""
+}
params.bigwig_to_wig = ""
params.bigwig_to_wig_out = ""
--
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