Commit 48d7e8b0 authored by fduveau's avatar fduveau
Browse files

Update src/RNASeq.nf

parent 496e6480
......@@ -24,19 +24,20 @@ process adaptor_removal {
}
process trimming {
tag "$pair_id"
tag "${reads}"
publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
output:
set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
script:
"""
cutadapt -q 20,20 \
-o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
"""
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
"""
}
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