process KRONA_KTIMPORTTEXT { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::krona=2.8.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1': 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }" input: tuple val(meta), path(report) output: tuple val(meta), path ('*.html'), emit: html path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ ktImportText \\ $args \\ -o ${prefix}.html \\ $report cat <<-END_VERSIONS > versions.yml "${task.process}": krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g') END_VERSIONS """ }