Verified Commit a97e28f0 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

urqt.nf: improve input

parent 52d58451
......@@ -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
"""
}
......
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