kkonganti@0: process MASURCA_POLISH {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_micro'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}masurca${params.fs}4.1.0" : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::masurca=4.1.0 conda-forge::libgcc-ng" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/masurca:4.1.0--pl5321hb5bd705_1' :
kkonganti@0:         'quay.io/biocontainers/masurca:4.1.0--pl5321hb5bd705_1' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(contigs), path(reads)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("${prefix}_contigs.fa"), emit: polished
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:         def mem_per_thread = task.memory.toGiga().toInteger().div(task.cpus.toInteger()).round(0)
kkonganti@0:         def all_reads      = "${reads.join(' ')}"
kkonganti@0:         prefix             = (task.ext.prefix ?: meta.id)
kkonganti@0:         """
kkonganti@0:         polca.sh \\
kkonganti@0:             -a $contigs \\
kkonganti@0:             -r '${all_reads}' \\
kkonganti@0:             -t $task.cpus \\
kkonganti@0:             -m $mem_per_thread \\
kkonganti@0:             $args \\
kkonganti@0:         
kkonganti@0:         mv 'contigs.fa' "${prefix}.contigs.fa"
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             masurca: \$(echo \$(masurca --version 2>&1) | sed 's/^.*version //')
kkonganti@0:         END_VERSIONS
kkonganti@0:     """
kkonganti@0: }