kkonganti@11: process OTF_GENOME {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label "process_pico"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/python:3.10.4' :
kkonganti@11:         'quay.io/biocontainers/python:3.10.4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(kma_hits), path(kma_fragz)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true
kkonganti@11:         tuple val(meta), path('*_aln_reads.fna.gz')         , emit: reads_extracted, optional: true
kkonganti@11:         path '*FAILED.txt'                                  , emit: failed, optional: true
kkonganti@11:         path 'versions.yml'                                 , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = task.ext.args ?: ''
kkonganti@11:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         args += (kma_hits ? " -txt ${kma_hits}" : '')
kkonganti@11:         args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '')
kkonganti@11:         args += (prefix ? " -op ${prefix}" : '')
kkonganti@11: 
kkonganti@11:         """
kkonganti@11:         gen_otf_genome.py \\
kkonganti@11:             $args
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             python: \$( python --version | sed 's/Python //g' )
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }