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1 process PIRATE {
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2 tag "$meta.id"
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3 label 'process_medium'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}pirate${params.fs}5.2.0" : null)
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6 conda (params.enable_conda ? "bioconda::pirate=1.0.5 bioconda::mcl=14.137 conda-forge::r-dplyr" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' :
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9 'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }"
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10
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11 input:
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12 tuple val(meta), path(gff)
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13
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14 output:
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15 tuple val(meta), path("results/*") , emit: results
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16 tuple val(meta), path("results/core_alignment.fasta"), emit: aln, optional: true
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 def rplots = (params.enable_conda ? '--rplots' : '')
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26 """
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27 PIRATE \\
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28 $args \\
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29 $rplots \\
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30 --threads $task.cpus \\
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31 --input ".${params.fs}" \\
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32 --output results/
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33
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34 cat <<-END_VERSIONS > versions.yml
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35 "${task.process}":
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36 pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
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37 END_VERSIONS
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38 """
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39 } |
