From 47eba2c496b8c0406fbfd1da798531e8e8a3388f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 14:48:21 +0200
Subject: [PATCH] ucsc: add wigtobigwig convertion
---
src/nf_modules/ucsc/main.nf | 45 +++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 6e0c016d..e3076ebd 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -78,4 +78,49 @@ bedgraph_to_wig.pl --bedgraph ${bw_a.simpleName}.bg --wig ${bw_a.simpleName}.wig
bigWigToBedGraph ${bw_b} ${bw_b.simpleName}.bg
bedgraph_to_wig.pl --bedgraph ${bw_b.simpleName}.bg --wig ${bw_b.simpleName}.wig --step 10
"""
+}
+
+params.wig_to_bigwig = ""
+params.wig_to_bigwig_out = ""
+process wig_to_bigwig {
+ container = "${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(w)
+
+ output:
+ tuple val(file_id), path("${bw.simpleName}.bw"), emit: bw
+
+ script:
+"""
+wigToBigWig ${w} ${w.simpleName}.bw
+"""
+}
+
+params.wig2_to_bigwig2 = ""
+params.wig2_to_bigwig2_out = ""
+process wig2_to_bigwig2 {
+ container = "${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(w_a), path(w_b)
+
+ output:
+ tuple val(file_id), path("${bw_a.simpleName}.bw"), path("${bw_b.simpleName}.bw"), emit: bw
+
+ script:
+"""
+wigToBigWig ${w_a} ${w_a.simpleName}.bw
+wigToBigWig ${w_b} ${w_b.simpleName}.bw
+"""
}
\ No newline at end of file
--
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