process ABACAS { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::abacas=1.3.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/abacas:1.3.1--pl526_0' : 'quay.io/biocontainers/abacas:1.3.1--pl526_0' }" input: tuple val(meta), path(scaffold) path fasta output: tuple val(meta), path('*.abacas*'), emit: results 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}" """ abacas.pl \\ -r $fasta \\ -q $scaffold \\ $args \\ -o ${prefix}.abacas mv nucmer.delta ${prefix}.abacas.nucmer.delta mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta mv nucmer.tiling ${prefix}.abacas.nucmer.tiling mv unused_contigs.out ${prefix}.abacas.unused.contigs.out cat <<-END_VERSIONS > versions.yml "${task.process}": abacas: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//') END_VERSIONS """ }