From 9cc39469f9c4d621d8d159b59b1a585179cf5025 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 25 Jan 2021 17:35:21 +0100
Subject: [PATCH] bedtools: add bam_id val
---
src/nf_modules/bedtools/main.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index f55991eb..4d3e4e1f 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -24,14 +24,14 @@ bedtools getfasta -name \
process bam_to_fastq_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
- tag "${bam.baseName}"
+ tag "${bam_id}"
publishDir "results/mapping/fastq/", mode: 'copy'
input:
- path bam
+ tuple val(bam_id), path(bam)
output:
- tuple val(bam.baseName), path("*.fastq"), emit: fastq
+ tuple val(bam_id), path("*.fastq"), emit: fastq
script:
"""
@@ -43,11 +43,11 @@ bedtools bamtofastq \
process bam_to_fastq_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
- tag "${bam.baseName}"
+ tag "${bam_id}"
publishDir "results/mapping/fastq/", mode: 'copy'
input:
- path bam
+ tuple val(bam_id), path(bam)
output:
tuple val(bam.baseName), path("*.fastq"), emit: fastq
--
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