kkonganti@105: process SPADES_ASSEMBLE {
kkonganti@105:     tag "$meta.id"
kkonganti@105:     label 'process_higher'
kkonganti@105: 
kkonganti@105:     module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null)
kkonganti@105:     conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
kkonganti@105:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@105:         'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
kkonganti@105:         'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
kkonganti@105: 
kkonganti@105:     input:
kkonganti@105:     tuple val(meta), path(illumina), path(pacbio), path(nanopore)
kkonganti@105: 
kkonganti@105:     output:
kkonganti@105:     path "${meta.id}${params.fs}*"
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true
kkonganti@105:     tuple val(meta), path("${meta.id}${params.fs}spades.log")     , emit: log
kkonganti@105:     path  "versions.yml"                                          , emit: versions
kkonganti@105: 
kkonganti@105:     when:
kkonganti@105:     task.ext.when == null || task.ext.when
kkonganti@105: 
kkonganti@105:     script:
kkonganti@105:     def args = task.ext.args ?: ''
kkonganti@105:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@105:     def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : ""
kkonganti@105:     def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
kkonganti@105:     def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
kkonganti@105:     def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
kkonganti@105:     def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : ""
kkonganti@105:     """
kkonganti@105:     spades.py \\
kkonganti@105:         $args \\
kkonganti@105:         --threads $task.cpus \\
kkonganti@105:         $maxmem \\
kkonganti@105:         $custom_hmms \\
kkonganti@105:         $illumina_reads \\
kkonganti@105:         $pacbio_reads \\
kkonganti@105:         $nanopore_reads \\
kkonganti@105:         -o ${prefix}
kkonganti@105: 
kkonganti@105:     cat <<-END_VERSIONS > versions.yml
kkonganti@105:     "${task.process}":
kkonganti@105:         spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
kkonganti@105:     END_VERSIONS
kkonganti@105:     """
kkonganti@105: }