process UNICYCLER { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : 'quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3' }" input: tuple val(meta), path(shortreads), path(longreads) output: tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : "" def long_reads = longreads ? "-l $longreads" : "" """ unicycler \\ --threads $task.cpus \\ $args \\ $short_reads \\ $long_reads \\ --out ./ mv assembly.fasta ${prefix}.scaffolds.fa gzip -n ${prefix}.scaffolds.fa mv assembly.gfa ${prefix}.assembly.gfa gzip -n ${prefix}.assembly.gfa mv unicycler.log ${prefix}.unicycler.log cat <<-END_VERSIONS > versions.yml "${task.process}": unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//') END_VERSIONS """ }