kkonganti@0: process SHOVILL {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_low'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}shovill${params.fs}1.1.0" : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::shovill=1.1.0 conda-forge::pigz" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' :
kkonganti@0:         'quay.io/biocontainers/shovill:1.1.0--0' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(reads)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("${prefix}${params.fs}contigs.fa")                         , emit: contigs
kkonganti@0:         tuple val(meta), path("${prefix}${params.fs}shovill.corrections")                , emit: corrections
kkonganti@0:         tuple val(meta), path("${prefix}${params.fs}shovill.log")                        , emit: log
kkonganti@0:         tuple val(meta), path("${prefix}${params.fs}{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
kkonganti@0:         tuple val(meta), path("${prefix}${params.fs}contigs.{fastg,gfa,LastGraph}")      , emit: gfa, optional: true
kkonganti@0:         path "versions.yml"                                                              , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         def memory = task.memory.toGiga()
kkonganti@0:         prefix = (task.ext.prefix ?: meta.id)
kkonganti@0:         """
kkonganti@0:         shovill \\
kkonganti@0:             --R1 ${reads[0]} \\
kkonganti@0:             --R2 ${reads[1]} \\
kkonganti@0:             $args \\
kkonganti@0:             --cpus $task.cpus \\
kkonganti@0:             --ram $memory \\
kkonganti@0:             --outdir $prefix \\
kkonganti@0:             --force
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
kkonganti@0:         END_VERSIONS
kkonganti@0:     """
kkonganti@0: }