process SISTR { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2': 'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("*.tab") , emit: tsv tuple val(meta), path("*-allele.fasta"), emit: allele_fasta tuple val(meta), path("*-allele.json") , emit: allele_json tuple val(meta), path("*-cgmlst.csv") , emit: cgmlst_csv 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 sistr \\ --qc \\ $args \\ --threads $task.cpus \\ --alleles-output ${prefix}-allele.json \\ --novel-alleles ${prefix}-allele.fasta \\ --cgmlst-profiles ${prefix}-cgmlst.csv \\ --output-prediction ${prefix} \\ --output-format tab \\ $fasta_name cat <<-END_VERSIONS > versions.yml "${task.process}": sistr: \$(echo \$(sistr --version 2>&1) | sed 's/^.*sistr_cmd //; s/ .*\$//' ) END_VERSIONS """ }