From f5ded041d84709b5769bc4126bc81f518051c9a6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 10:46:00 +0200
Subject: [PATCH] ucsc: add bedgraph_to_wig.pl script
---
src/.docker_modules/ucsc/407/Dockerfile | 3 ++
src/nf_modules/ucsc/main.nf | 49 +++++++++++++++++++++++++
2 files changed, 52 insertions(+)
diff --git a/src/.docker_modules/ucsc/407/Dockerfile b/src/.docker_modules/ucsc/407/Dockerfile
index 1499bdb1..b0c01263 100644
--- a/src/.docker_modules/ucsc/407/Dockerfile
+++ b/src/.docker_modules/ucsc/407/Dockerfile
@@ -25,3 +25,6 @@ cd .. &&\
mv userApps/bin/* /usr/bin/ &&\
rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
rm -R userApps
+
+COPY bedgraph_to_wig.pl /usr/bin/
+RUN chmod +x /usr/bin/bedgraph_to_wig.pl
\ No newline at end of file
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index f193f047..5b203c8e 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -30,3 +30,52 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \
${bg.simpleName}_norm.bw
"""
}
+
+
+params.bigwig_to_wig = ""
+params.bigwig_to_wig_out = ""
+process bigwig_to_wig {
+ container = "${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:
+"""
+bigWigToBedGraph ${bw} ${bw.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw.simpleName}.bg --wig ${bw.simpleName}.wig --step 1
+"""
+}
+
+params.bigwig2_to_wig2 = ""
+params.bigwig2_to_wig2_out = ""
+process bigwig2_to_wig2 {
+ container = "${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:
+"""
+bigWigToBedGraph ${bw_a} ${bw_a.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw_a.simpleName}.bg --wig ${bw_a.simpleName}.wig --step 1
+bigWigToBedGraph ${bw_b} ${bw_b.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw_b.simpleName}.bg --wig ${bw_b.simpleName}.wig --step 1
+"""
+}
\ No newline at end of file
--
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