process MEDAKA { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' : 'quay.io/biocontainers/medaka:1.4.4--py38h130def0_0' }" input: tuple val(meta), path(reads), path(assembly) output: tuple val(meta), path("*.fa.gz"), emit: assembly 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}" """ medaka_consensus \\ -t $task.cpus \\ $args \\ -i $reads \\ -d $assembly \\ -o ./ mv consensus.fasta ${prefix}.fa gzip -n ${prefix}.fa cat <<-END_VERSIONS > versions.yml "${task.process}": medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' ) END_VERSIONS """ }