From 42e06407ef76155cf51d1dadac96f8e375a8e274 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 18 Oct 2021 16:07:55 +0200
Subject: [PATCH] ucsc: add wig2bedgraph process
---
src/nf_modules/ucsc/main.nf | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 6ce54f0d..06ac54f0 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -35,6 +35,28 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \
"""
}
+params.wig2bedgraph = ""
+params.wig2bedgraph_out = ""
+process wig2bedgraph {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${file_id}"
+ if (params.wig2bedgraph_out != "") {
+ publishDir "results/${params.wig2bedgraph_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id) path(wig)
+
+ output:
+ tuple val(file_id), path("*.bg"), emit: bedgraph
+
+ script:
+"""
+wigToBedGraph ${wig} ${wig.simpleName}.bg
+"""
+}
+
params.wig_to_bedgraph = ""
params.wig_to_bedgraph_out = ""
process wig_to_bedgraph {
--
GitLab