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1 process DOWNLOAD_PDG_METADATA {
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2 tag "dl_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 val pdg_release
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13
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14 output:
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15 path "**${params.fs}*.metadata.tsv" , emit: pdg_metadata
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16 path "**${params.fs}*.reference_target.cluster_list.tsv", emit: snp_cluster_metadata
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17 path "**${params.fs}*accs_all.txt" , emit: accs
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18 path 'versions.yml' , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 args += (pdg_release ? " -rel ${pdg_release}" : '')
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26 args += (params.pdg_org ? " -org ${params.pdg_org}" : '')
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27 """
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28 dl_pdg_metadata.py \\
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29 $args
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 python: \$( python --version | sed 's/Python //g' )
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34 END_VERSIONS
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35 """
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36
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37 } |
