From 59c1681f16cfc7e56de5adcb6d6916618ef150b3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 15:05:28 +0200
Subject: [PATCH] ucsc: rm non working BigWigToWig convertion (see bioconvert)
---
src/nf_modules/ucsc/main.nf | 54 -------------------------------------
1 file changed, 54 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 999f55fb..f193f047 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -30,57 +30,3 @@ 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:
-"""
-bigWigToWig ${params.bigwig_to_wig} \
- ${bw} \
- ${bg.simpleName}.raw
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.raw > ${bw.simpleName}.wig
-"""
-}
-
-params.bigwig2_to_wig2 = ""
-params.bigwig2_to_wig2_out = ""
-process bigwig2_to_wig2 {
- container = "${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:
-"""
-bigWigToWig ${params.bigwig_to_wig} \
- ${bw_a} \
- ${bw_a.simpleName}.raw
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.raw > ${bw_a.simpleName}.wig
-bigWigToBedGraph ${params.bigwig_to_wig} \
- ${bw_b} \
- ${bw_b.simpleName}.raw
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.raw > ${bw_b.simpleName}.wig
-"""
-}
\ No newline at end of file
--
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