kkonganti@11: process INDEX_PDG_METADATA {
kkonganti@11:     tag "index_pdg_metadata.py"
kkonganti@11:     label "process_pico"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/python:3.10.4' :
kkonganti@11:         'quay.io/biocontainers/python:3.10.4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         path pdg_metadata
kkonganti@11:         path pdg_ref_snp_metadata
kkonganti@11:         path accs_all
kkonganti@11:         path mlst_results
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         path "*.pickle"    , emit: index
kkonganti@11:         path 'versions.yml', emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = task.ext.args ?: ''
kkonganti@11:         def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
kkonganti@11:         """
kkonganti@11:         index_pdg_metadata.py \\
kkonganti@11:             $mlst_results \\
kkonganti@11:             -pdg_dir "."
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             python: \$( python --version | sed 's/Python //g' )
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: 
kkonganti@11: }