kkonganti@17: process MASH_SKETCH {
kkonganti@17:     tag "mash sketch"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
kkonganti@17:         'quay.io/biocontainers/mash:2.3--he348c14_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(query), path(genomes_dir)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("*.msh")               , emit: sketch
kkonganti@17:         tuple val(meta), path("*_mash_sketch.status"), emit: stats
kkonganti@17:         path "versions.yml"                          , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         def queries = (query ?: query.collect().join(' '))
kkonganti@17:         sleep(Math.round(params.genomes_chunk.toInteger()) as int * 600)
kkonganti@17:         """
kkonganti@17:         mash \\
kkonganti@17:             sketch \\
kkonganti@17:             -p $task.cpus \\
kkonganti@17:             -o "msh.k${params.mashsketch_k}.${params.mashsketch_s}h.${prefix}" \\
kkonganti@17:             $args \\
kkonganti@17:             $queries \\
kkonganti@17:             2> ${prefix}_mash_sketch.status
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             mash: \$( mash --version )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }