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1 process PROKKA {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}prokka${params.fs}1.14.5" : null)
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6 conda (params.enable_conda ? "bioconda::prokka=1.14.6 conda-forge::perl" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
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9 'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
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10
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11 input:
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12 tuple val(meta), path(fasta), path(proteins), path(prodigal_tf)
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13
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14 output:
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15 tuple val(meta), path("${prefix}/*.gff"), emit: gff
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16 tuple val(meta), path("${prefix}/*.gbk"), emit: gbk
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17 tuple val(meta), path("${prefix}/*.fna"), emit: fna
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18 tuple val(meta), path("${prefix}/*.faa"), emit: faa
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19 tuple val(meta), path("${prefix}/*.ffn"), emit: ffn
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20 tuple val(meta), path("${prefix}/*.sqn"), emit: sqn
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21 tuple val(meta), path("${prefix}/*.fsa"), emit: fsa
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22 tuple val(meta), path("${prefix}/*.tbl"), emit: tbl
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23 tuple val(meta), path("${prefix}/*.err"), emit: err
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24 tuple val(meta), path("${prefix}/*.log"), emit: log
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25 tuple val(meta), path("${prefix}/*.txt"), emit: txt
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26 tuple val(meta), path("${prefix}/*.tsv"), emit: tsv
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27 path "versions.yml" , emit: versions
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28
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29 when:
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30 task.ext.when == null || task.ext.when
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31
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32 script:
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33 def args = task.ext.args ?: ''
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34 def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
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35 def prodigal_tf = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
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36 def prefix_l = "${meta.id}" ?: ''
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37 prefix = task.ext.prefix ?: "${meta.id}"
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38 def strain = !params.prokka_strain && prefix_l ? "--strain '${prefix_l}'" : ''
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39
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40 """
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41 prokka \\
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42 $strain \\
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43 $args \\
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44 --cpus $task.cpus \\
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45 --prefix $prefix \\
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46 $proteins_opt \\
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47 $prodigal_tf \\
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48 $fasta
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49
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50 cat <<-END_VERSIONS > versions.yml
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51 "${task.process}":
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52 prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
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53 END_VERSIONS
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54 """
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55 } |
