From f1a4012f9305c7815b104832f94547677065e6a9 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 26 Oct 2021 14:40:56 +0200
Subject: [PATCH] danpos: add dpos_bw_no_b process
---
src/nf_modules/danpos/main.nf | 60 +++++++++++++++++++++++++++++++++++
1 file changed, 60 insertions(+)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 99ff55dc..93d332cc 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -134,6 +134,66 @@ awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$2-1, \$3, "Interval_"NR-1, \$
"""
}
+workflow dpos_bw_no_b {
+ take:
+ fasta
+ fastq
+ bw
+ main:
+ bigwig_to_wig(bw)
+ dpos_wig_no_b(fastq, bigwig_to_wig.out.wig)
+ wig_to_bedgraph(fasta, bigwig_to_wig.out.wig)
+
+ emit:
+ bg = wig_to_bedgraph.out.bg
+ wig = bigwig_to_wig.out.wig
+ bed = dpos_wig.out.bed
+}
+
+process dpos_wig {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+ if (params.dpos_out != "") {
+ publishDir "results/${params.dpos_out}", mode: 'copy', overwrite: true
+ }
+
+ input:
+ val fastq
+ tuple val(file_id), path(wig_ip), path(wig_wce)
+
+ output:
+ tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
+
+ script:
+
+ switch(file_id) {
+ case {it instanceof List}:
+ file_prefix = file_id[0]
+ break
+ case {it instanceof Map}:
+ file_prefix = file_id.values()[0]
+ break
+ default:
+ file_prefix = file_id
+ break
+ }
+
+ m = 0
+ if (fastq[1].size() == 2){
+ m = 1
+ }
+"""
+danpos.py dpos -m ${m} \
+ ${params.dpos} \
+ -o ${file_prefix} \
+ ${wig_ip}
+mv ${file_prefix}/pooled/* ${file_prefix}/
+rm -R ${file_prefix}/pooled
+awk -v FS='\t' -v OFS='\t' 'FNR > 1 { print \$1, \$2-1, \$3, "Interval_"NR-1, \$6, "+" }' ${file_prefix}/${wig_ip.simpleName}.positions.xls > ${file_prefix}/${wig_ip.simpleName}.positions.bed
+"""
+}
+
workflow dwig_bwvsbw {
take:
fasta
--
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