def VERSION = '1.0.1' // Version information not provided by tool on CLI process HPSUISSERO { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0': 'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.tsv"), emit: tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def is_compressed = fasta.getName().endsWith(".gz") ? true : false def fasta_name = fasta.getName().replace(".gz", "") """ if [ "$is_compressed" == "true" ]; then gzip -c -d $fasta > $fasta_name fi HpsuisSero.sh \\ -i $fasta_name \\ -o ./ \\ -s $prefix \\ -x fasta \\ -t $task.cpus cat <<-END_VERSIONS > versions.yml "${task.process}": hpsuissero: $VERSION END_VERSIONS """ }