Skip to content
Snippets Groups Projects
Verified Commit a8f12adc authored by Laurent Modolo's avatar Laurent Modolo
Browse files

add kmc module

parent 8de7eee0
No related merge requests found
/*
* normalize bam file
*/
process FASTKMERS {
tag "$meta.id"
label 'process_single'
publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/kmc:3.2.2"
input:
tuple val(meta), path(fastq)
output:
tuple val(meta), path("*.csv"), emit: csv
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
kmc -k31 ${fastq} 31mers .
kmc_tools transform 27mers dump ${fastq.simpleName}.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kmc: \$(echo \$(kmc --version 2>&1))
END_VERSIONS
"""
}
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment