kkonganti@0: process MASH_SCREEN {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_micro'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null)
kkonganti@0:     conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
kkonganti@0:         'quay.io/biocontainers/mash:2.3--he348c14_1' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(query)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("*.screened"), emit: screened
kkonganti@0:         path "versions.yml"                , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0:         def sequence_sketch = (meta.sequence_sketch ?: '')
kkonganti@0:         """
kkonganti@0:         mash \\
kkonganti@0:             screen \\
kkonganti@0:             $args \\
kkonganti@0:             -p $task.cpus \\
kkonganti@0:             $sequence_sketch \\
kkonganti@0:             $query \\
kkonganti@0:             > ${prefix}.screened
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             mash: \$( mash --version )
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }