kkonganti@17: process MEGAHIT_ASSEMBLE {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::python bioconda::megahit=1.2.9" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
kkonganti@17:         'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(reads)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, optional: true
kkonganti@17:         path "versions.yml"                                                 , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         def maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : ""
kkonganti@17:         if (meta.single_end) {
kkonganti@17:             """
kkonganti@17:             megahit \\
kkonganti@17:                 -r ${reads} \\
kkonganti@17:                 -t $task.cpus \\
kkonganti@17:                 $maxmem \\
kkonganti@17:                 $args \\
kkonganti@17:                 --out-dir $prefix \\
kkonganti@17:                 --out-prefix $prefix
kkonganti@17: 
kkonganti@17:             cat <<-END_VERSIONS > versions.yml
kkonganti@17:             "${task.process}":
kkonganti@17:                 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
kkonganti@17:             END_VERSIONS
kkonganti@17:             """
kkonganti@17:         } else {
kkonganti@17:             """
kkonganti@17:             megahit \\
kkonganti@17:                 -1 ${reads[0]} \\
kkonganti@17:                 -2 ${reads[1]} \\
kkonganti@17:                 -t $task.cpus \\
kkonganti@17:                 $maxmem \\
kkonganti@17:                 $args \\
kkonganti@17:                 --out-dir $prefix \\
kkonganti@17:                 --out-prefix $prefix
kkonganti@17: 
kkonganti@17:             cat <<-END_VERSIONS > versions.yml
kkonganti@17:             "${task.process}":
kkonganti@17:                 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
kkonganti@17:             END_VERSIONS
kkonganti@17:             """
kkonganti@17:     }
kkonganti@17: }