process CHECKM_LINEAGEWF { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::checkm-genome=1.1.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1' : 'quay.io/biocontainers/checkm-genome:1.1.3--py_1' }" input: tuple val(meta), path(fasta) val fasta_ext output: tuple val(meta), path("${prefix}") , emit: checkm_output tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ checkm \\ lineage_wf \\ -t $task.cpus \\ -f ${prefix}.tsv \\ --tab_table \\ --pplacer_threads $task.cpus \\ -x $fasta_ext \\ $args \\ . \\ $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' ) END_VERSIONS """ }