process MINIASM { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' : 'quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2' }" input: tuple val(meta), path(reads), path(paf) output: tuple val(meta), path("*.gfa.gz") , emit: gfa tuple val(meta), path("*.fasta.gz"), emit: assembly path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ miniasm \\ $args \\ -f $reads \\ $paf > \\ ${prefix}.gfa awk '/^S/{print ">"\$2"\\n"\$3}' "${prefix}.gfa" | fold > ${prefix}.fasta gzip -n ${prefix}.gfa gzip -n ${prefix}.fasta cat <<-END_VERSIONS > versions.yml "${task.process}": miniasm: \$( miniasm -V 2>&1 ) END_VERSIONS """ }