kkonganti@17: process INDEX_METADATA {
kkonganti@17:     tag "get_top_unique_mash_hit_genomes.py"
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(type), path(sero_tbl)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         path '*.ACC2SERO.pickle', emit: acc2sero
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 = (
kkonganti@17:             type.find(/_comp/) \
kkonganti@17:             ? type.replaceAll(/\_comp/, 'per_comp_serotype') \
kkonganti@17:             : type.replaceAll(/\_snp/, 'per_snp_cluster')
kkonganti@17:         )
kkonganti@17:         """
kkonganti@17:         get_top_unique_mash_hit_genomes.py \\
kkonganti@17:             -s $sero_tbl -op $prefix
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             python: \$( python --version | sed 's/Python //g' )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }