process DASTOOL_SCAFFOLDS2BIN { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' : 'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }" input: tuple val(meta), path(fasta) val(extension) output: tuple val(meta), path("*.tsv"), emit: scaffolds2bin 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 file_extension = extension ? extension : "fasta" def clean_fasta = fasta.toString() - ".gz" def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta" """ $decompress_fasta Fasta_to_Scaffolds2Bin.sh \\ $args \\ -i . \\ -e $file_extension \\ > ${prefix}.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool version //' ) END_VERSIONS """ }