kkonganti@105: process MEGAHIT_ASSEMBLE {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_higher'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
kkonganti@105:     conda (params.enable_conda ? "bioconda::megahit=1.2.9" : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
kkonganti@105:         'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(reads)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, optional: true
kkonganti@105:     path "versions.yml"                                                 , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     def maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : ""
kkonganti@105:     if (meta.single_end) {
kkonganti@105:         """
kkonganti@105:         megahit \\
kkonganti@105:             -r ${reads} \\
kkonganti@105:             -t $task.cpus \\
kkonganti@105:             $maxmem \\
kkonganti@105:             $args \\
kkonganti@105:             --out-dir $prefix \\
kkonganti@105:             --out-prefix $prefix
kkonganti@105: 
kkonganti@105:         cat <<-END_VERSIONS > versions.yml
kkonganti@105:         "${task.process}":
kkonganti@105:             megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
kkonganti@105:         END_VERSIONS
kkonganti@105:         """
kkonganti@105:     } else {
kkonganti@105:         """
kkonganti@105:         megahit \\
kkonganti@105:             -1 ${reads[0]} \\
kkonganti@105:             -2 ${reads[1]} \\
kkonganti@105:             -t $task.cpus \\
kkonganti@105:             $maxmem \\
kkonganti@105:             $args \\
kkonganti@105:             --out-dir $prefix \\
kkonganti@105:             --out-prefix $prefix
kkonganti@105: 
kkonganti@105:         cat <<-END_VERSIONS > versions.yml
kkonganti@105:         "${task.process}":
kkonganti@105:             megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
kkonganti@105:         END_VERSIONS
kkonganti@105:         """
kkonganti@105:     }
kkonganti@105: }