kkonganti@0: process INDEX_PDG_METADATA {
kkonganti@0:     tag "index_pdg_metadata.py"
kkonganti@0:     label "process_pico"
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@0:     conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/python:3.10.4' :
kkonganti@0:         'quay.io/biocontainers/python:3.10.4' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         path pdg_metadata
kkonganti@0:         path pdg_ref_snp_metadata
kkonganti@0:         path accs_all
kkonganti@0:         path mlst_results
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         path "*.pickle"    , emit: index
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 mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
kkonganti@0:         """
kkonganti@0:         index_pdg_metadata.py \\
kkonganti@0:             $mlst_results \\
kkonganti@0:             -pdg_dir "."
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             python: \$( python --version | sed 's/Python //g' )
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: 
kkonganti@0: }