kkonganti@0: process PIRATE {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_medium'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? "${params.swmodulepath}${params.fs}pirate${params.fs}5.2.0" : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::pirate=1.0.5 bioconda::mcl=14.137 conda-forge::r-dplyr" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' :
kkonganti@0:         'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:         tuple val(meta), path(gff)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:         tuple val(meta), path("results/*")                   , emit: results
kkonganti@0:         tuple val(meta), path("results/core_alignment.fasta"), emit: aln, optional: true
kkonganti@0:         path "versions.yml"                                  , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:         task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:         def args = task.ext.args ?: ''
kkonganti@0:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0:         def rplots = (params.enable_conda ? '--rplots' : '')
kkonganti@0:         """
kkonganti@0:         PIRATE \\
kkonganti@0:             $args \\
kkonganti@0:             $rplots \\
kkonganti@0:             --threads $task.cpus \\
kkonganti@0:             --input ".${params.fs}" \\
kkonganti@0:             --output results/
kkonganti@0: 
kkonganti@0:         cat <<-END_VERSIONS > versions.yml
kkonganti@0:         "${task.process}":
kkonganti@0:             pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
kkonganti@0:         END_VERSIONS
kkonganti@0:         """
kkonganti@0: }