From a97e28f0a53ae5174c61fd856610717695f67be6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 10:49:36 +0200
Subject: [PATCH] urqt.nf: improve input
---
src/nf_modules/UrQt/urqt.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
index 85247d9..165af95 100644
--- a/src/nf_modules/UrQt/urqt.nf
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -19,12 +19,12 @@ Channel
.set { fastq_files }
process trimming {
- tag "$pair_id"
+ tag "${reads}"
cpus 4
publishDir "results/fastq/trimming/", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files
+ file reads from fastq_files
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
@@ -33,8 +33,8 @@ process trimming {
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
---out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
-> ${pair_id}_trimming_report.txt
+--out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
+> ${reads[0].baseName}_trimming_report.txt
"""
}
--
GitLab