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1 process PRODIGAL {
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2 tag "$meta.id"
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3 label 'process_nano'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}prodigal${params.fs}2.6.3" : null)
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6 conda (params.enable_conda ? "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
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9 'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
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10
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11 input:
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12 tuple val(meta), path(genome)
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13 val(output_format)
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14
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15 output:
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16 tuple val(meta), path("*.${output_format}"), emit: gene_annotations
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17 tuple val(meta), path("*.fna") , emit: cds
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18 tuple val(meta), path("*.faa") , emit: proteins
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19 tuple val(meta), path("*_all.txt") , emit: all_gene_annotations
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20 tuple val(meta), path("*trn") , emit: trained, optional: true
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21 path "versions.yml" , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def prefix = task.ext.prefix ?: "${meta.id}"
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29 def training = args.toString().matches(/.*-t/) ? "-t ${prefix}.trn" : ''
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30 args = args.toString().replace(/-t/, '')
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31 """
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32 if [ "$training" = "-t ${prefix}.trn" ]; then
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33 touch "${prefix}.fna"
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34 touch "${prefix}.faa"
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35 touch "${prefix}_all.txt"
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36 touch "${prefix}.${output_format}"
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37
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38 prodigal \\
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39 $training \\
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40 -i $genome
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41 fi
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42
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43 prodigal \\
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44 $args \\
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45 -d "${prefix}.fna" \\
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46 -o "${prefix}.${output_format}" \\
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47 -a "${prefix}.faa" \\
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48 -s "${prefix}_all.txt" \\
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49 -i $genome
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50
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51 cat <<-END_VERSIONS > versions.yml
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52 "${task.process}":
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53 prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
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54 END_VERSIONS
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55 """
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56 } |
