process CENTRIFUGE_KREPORT { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6': 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" input: tuple val(meta), path(results) path db output: tuple val(meta), path('*.txt') , emit: kreport 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}" """ db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'` centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //') END_VERSIONS """ }