process SEQSERO2 { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }" input: tuple val(meta), path(seqs) output: tuple val(meta), path("results/*_log.txt") , emit: log tuple val(meta), path("results/*_result.tsv"), emit: tsv tuple val(meta), path("results/*_result.txt"), emit: txt path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ SeqSero2_package.py \\ $args \\ -d results/ \\ -n $prefix \\ -p $task.cpus \\ -i $seqs cat <<-END_VERSIONS > versions.yml "${task.process}": seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' ) END_VERSIONS """ }