From 759a77c9cc1155d40bcfff89cd508f171944ea7e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 15:04:48 +0200
Subject: [PATCH] bioconvert: add main.nf
---
src/nf_modules/bioconvert/main.nf | 46 +++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
create mode 100644 src/nf_modules/bioconvert/main.nf
diff --git a/src/nf_modules/bioconvert/main.nf b/src/nf_modules/bioconvert/main.nf
new file mode 100644
index 00000000..92925351
--- /dev/null
+++ b/src/nf_modules/bioconvert/main.nf
@@ -0,0 +1,46 @@
+version = "0.4.3"
+container_url = "lbmc/bioconvert:${version}"
+params.bigwig_to_wig = ""
+params.bigwig_to_wig_out = ""
+process bigwig_to_wig {
+ container = "${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(bw)
+
+ output:
+ tuple val(file_id), path("*.wig"), emit: wig
+
+ script:
+"""
+bioconvert bigwig2wiggle ${bw} ${bw.simpleName}.wig
+"""
+}
+
+params.bigwig2_to_wig2 = ""
+params.bigwig2_to_wig2_out = ""
+process bigwig2_to_wig2 {
+ container = "${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(bw_a), path(bw_b)
+
+ output:
+ tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig
+
+ script:
+"""
+bioconvert bigwig2wiggle ${bw_a} ${bw_a.simpleName}.wig
+bioconvert bigwig2wiggle ${bw_b} ${bw_b.simpleName}.wig
+"""
+}
\ No newline at end of file
--
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