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1 process DOWNLOAD_PUBMLST_SCHEME {
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2 tag "dl_pubmlst_profiles_and_schemes.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 organism
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13
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14 output:
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15 path "${organism}" , emit: pubmlst_dir
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16 path 'versions.yml', emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 """
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24 dl_pubmlst_profiles_and_schemes.py \\
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25 -f \\
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26 $args
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27
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28 cat <<-END_VERSIONS > versions.yml
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29 "${task.process}":
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30 python: \$( python --version | sed 's/Python //g' )
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31 END_VERSIONS
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32 """
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33
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34 } |
