kkonganti@17: process TOP_UNIQUE_SEROVARS {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label "process_pico"
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/python:3.10.4' :
kkonganti@17:         'quay.io/biocontainers/python:3.10.4' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(mash_screen_res)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path('*_UNIQUE_HITS.txt')      , emit: tsv, optional: true
kkonganti@17:         tuple val(meta), path('*_UNIQUE_HITS_POPUP.txt'), emit: popup, optional: true
kkonganti@17:         tuple val(meta), path('*_UNIQUE_HITS_ACCS.txt') , emit: accessions, optional: true
kkonganti@17:         tuple val(meta), path('*_UNIQUE_HITS.fna.gz')   , emit: genomes_fasta, optional: true
kkonganti@17:         path'*FAILED.txt'                               , emit: failed, optional: true
kkonganti@17:         path 'versions.yml'                             , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         args += (mash_screen_res ? " -m ${mash_screen_res}" : '')
kkonganti@17:         args += (prefix ? " -op ${prefix}" : '')
kkonganti@17:         """
kkonganti@17:         get_top_unique_mash_hit_genomes.py \\
kkonganti@17:             $args
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             python: \$( python --version | sed 's/Python //g' )
kkonganti@17:             datasets: \$( datasets --version | sed 's/datasets version: //g' )
kkonganti@17:             dataformat: \$( dataformat version )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: 
kkonganti@17: }