kkonganti@0: process KRONA_KTIMPORTTEXT {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_nano'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}krona${params.fs}2.8.1" : null)
kkonganti@0:     conda (params.enable_conda ? "conda-forge::curl bioconda::krona=2.8.1" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
kkonganti@0:         'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(report)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path ('*.html'), emit: html
kkonganti@0:         path "versions.yml"             , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0:         def krona_suffix = params.krona_res_suffix ?: '.krona.tsv'
kkonganti@0:         def reports = report.collect {
kkonganti@0:             it = it.toString() + ',' + it.toString().replaceAll(/(.*)${krona_suffix}$/, /$1/)
kkonganti@0:         }.sort().join(' ')
kkonganti@0:         """
kkonganti@0:         ktImportText  \\
kkonganti@0:             $args \\
kkonganti@0:             -o ${prefix}.html \\
kkonganti@0:             $reports
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }