kkonganti@11: process POLYPOLISH {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_micro'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}polypolish${params.fs}0.5.0" : null)
kkonganti@11:     conda (params.enable_conda ? "bioconda::polypolish=0.5.0 conda-forge::libgcc-ng" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/polypolish:0.5.0--hdbdd923_4' :
kkonganti@11:         'quay.io/biocontainers/polypolish:0.5.0--hdbdd923_4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(genome), path(sam)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("*.polished.fa"), emit: polished
kkonganti@11:         path  "versions.yml"                  , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args   = task.ext.args ?: ''
kkonganti@11:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         """
kkonganti@11: 
kkonganti@11:         polypolish \\
kkonganti@11:             $args \\
kkonganti@11:             $genome \\
kkonganti@11:             ${sam.join(' ')} > ${prefix}.polished.fa
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             polypolish: \$(echo \$(polypolish -V 2>&1) | sed 's/^Polypolish v//')
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }