From ac7209acb6766ce4e6257bc9c69e9a2875a58b7e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Oct 2021 11:06:17 +0200
Subject: [PATCH] danpos: re-add wce for dpos_bam
---
src/nf_modules/danpos/main.nf | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 0d2ef78c..68d9b687 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -17,10 +17,10 @@ workflow dpos_bam_bg {
main:
dpos_bam(fastq, bam)
- wig_to_bedgraph(dpos_bam.out.wig)
+ wig2_to_bedgraph2(dpos_bam.out.wig)
emit:
- bedgraph = wig_to_bedgraph.out.bedgraph
+ bedgraph = wig2_to_bedgraph2.out.bedgraph
wig = dpos_bam.out.wig
bed = dpos_bam.out.bed
folder = dpos_bam.out.folder
@@ -36,10 +36,10 @@ process dpos_bam {
input:
tuple val(fastq_id), path(fastq)
- tuple val(file_id), path(bam_ip)
+ tuple val(file_id), path(bam_ip), path(bam_wce)
output:
- tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), emit: wig
+ tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), path("${file_prefix}/${bam_wce.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
@@ -64,6 +64,7 @@ process dpos_bam {
"""
danpos.py dpos -m ${m} \
${params.dpos} \
+ -b ${bam_wce}
-o ${file_prefix} \
${bam_ip}
mv ${file_prefix}/pooled/* ${file_prefix}/
--
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