mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
27 lines
663 B
Text
27 lines
663 B
Text
process cutadapt {
|
|
tag "${sample_id}"
|
|
|
|
container 'quay.io/biocontainers/cutadapt:1.16--py27_1'
|
|
|
|
input:
|
|
tuple sample_id, file(input_forward_fq), file(input_reverse_fq)
|
|
|
|
output:
|
|
tuple sample_id, file(forward_fq), file(reverse_fq)
|
|
|
|
script:
|
|
forward_fq = "trimmed_forward.fastq"
|
|
reverse_fq = "trimmed_reverse.fastq"
|
|
|
|
"""
|
|
cutadapt \
|
|
-j ${task.cpus} \
|
|
-q $params.cutadapt_min_quality \
|
|
--minimum-length $params.cutadapt_min_length \
|
|
--pair-filter=any \
|
|
--output ${forward_fq} \
|
|
--paired-output ${reverse_fq} '${input_forward_fq}' '${input_reverse_fq}'
|
|
|
|
cutadapt --version &> v_cutadapt.txt
|
|
"""
|
|
}
|