mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
37 lines
1 KiB
Text
37 lines
1 KiB
Text
process MASH_SKETCH {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
conda (params.enable_conda ? "bioconda::mash=2.3" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
|
|
'quay.io/biocontainers/mash:2.3--he348c14_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(reads)
|
|
|
|
output:
|
|
tuple val(meta), path("*.msh") , emit: mash
|
|
tuple val(meta), path("*.mash_stats") , emit: stats
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
mash \\
|
|
sketch \\
|
|
$args \\
|
|
-p $task.cpus \\
|
|
-o ${prefix} \\
|
|
-r $reads \\
|
|
2> ${prefix}.mash_stats
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
mash: \$(mash --version 2>&1)
|
|
END_VERSIONS
|
|
"""
|
|
}
|