Commit 240b4d6d authored by nfontrod's avatar nfontrod
Browse files

Rnaseq.nf : add trimming process

parent b04822b5
......@@ -24,3 +24,24 @@ process adaptor_removal {
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
process trimming {
tag "${reads}"
cpus 4
publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files_cut
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
--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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