29 lines
629 B
Text
29 lines
629 B
Text
process HAPLINK_SEQUENCES {
|
|
tag "${method}: ${prefix}"
|
|
label 'process_single'
|
|
label 'haplink'
|
|
|
|
container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
|
|
|
|
input:
|
|
tuple val(prefix), val(method), path(yaml)
|
|
path reference
|
|
|
|
output:
|
|
tuple val(prefix), val(method), path("*.fasta")
|
|
|
|
publishDir "${params.outdir}/${method}", mode: 'copy'
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
"""
|
|
export JULIA_NUM_THREADS=${task.cpus}
|
|
haplink sequences \\
|
|
"${reference}" \\
|
|
"${yaml}" \\
|
|
--prefix "${prefix}" \\
|
|
> "${prefix}.fasta"
|
|
"""
|
|
}
|