kkonganti@17: process BBTOOLS_BBMERGE {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}bbtools${params.fs}38.94" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::pbzip2 bioconda::bbmap=38.95" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/bbmap:38.95--he522d1c_0' :
kkonganti@17:         'quay.io/biocontainers/bbmap:38.95--he522d1c_0' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(reads)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("*.fastq.gz"), emit: fastq
kkonganti@17:         tuple val(meta), path("*.log")     , emit: log
kkonganti@17:         path "versions.yml"                , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         !meta.single_end
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@17:         def in_files = "in1=${reads[0]} in2=${reads[1]}"
kkonganti@17:         def out_file  = "out=${prefix}.bbmerge.fastq.gz"
kkonganti@17:         def adapters_file = file (meta.adapters)
kkonganti@17:         def adapters = !("${adapters_file.simpleName}" ==~ 'dummy_file.*') && adapters_file.exits() ? "adapters=${meta.adapters}" : ''
kkonganti@17:         def args_formatted = args.replaceAll('=\s+', '=')
kkonganti@17:         """
kkonganti@17:         bbmerge.sh \\
kkonganti@17:             -Xmx${task.memory.toGiga()}G \\
kkonganti@17:             threads=$task.cpus \\
kkonganti@17:             $args_formatted \\
kkonganti@17:             $adapters \\
kkonganti@17:             $in_files \\
kkonganti@17:             $out_file &> ${prefix}.bbmerge.log
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             bbmerge: \$( bbversion.sh )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: }