nf-core_modules/modules/mash/screen/main.nf

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2022-05-20 13:23:11 +00:00
process MASH_SCREEN {
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(query_sketch)
path fastx_db
output:
tuple val(meta), path("*.screen"), emit: screen
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 \\
screen \\
$args \\
-p $task.cpus \\
$query_sketch \\
$fastx_db \\
> ${prefix}.screen
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mash: \$( mash --version )
END_VERSIONS
"""
}