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1 process INDEX_PDG_METADATA {
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2 tag "index_pdg_metadata.py"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
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9 'quay.io/biocontainers/python:3.10.4' }"
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10
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11 input:
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12 path pdg_metadata
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13 path pdg_ref_snp_metadata
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14 path accs_all
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15 path mlst_results
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16
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17 output:
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18 path "*.pickle" , emit: index
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19 path 'versions.yml', emit: versions
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20
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21 when:
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22 task.ext.when == null || task.ext.when
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23
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24 script:
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25 def args = task.ext.args ?: ''
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26 def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
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27 """
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28 index_pdg_metadata.py \\
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29 $mlst_results \\
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30 -pdg_dir "."
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31
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32 cat <<-END_VERSIONS > versions.yml
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33 "${task.process}":
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34 python: \$( python --version | sed 's/Python //g' )
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35 END_VERSIONS
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36 """
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37
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38 } |
