Commit f51e613e authored by fduveau's avatar fduveau
Browse files

Update src/RNASeq.nf

parent af5d4955
......@@ -22,3 +22,21 @@ process adaptor_removal {
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
process trimming {
tag "$pair_id"
publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
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
"""
}
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