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1 process INDEX_METADATA {
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2 tag "get_top_unique_mash_hit_genomes.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 tuple val(type), path(sero_tbl)
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13
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14 output:
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15 path '*.ACC2SERO.pickle', emit: acc2sero
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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 def prefix = (
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24 type.find(/_comp/) \
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25 ? type.replaceAll(/\_comp/, 'per_comp_serotype') \
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26 : type.replaceAll(/\_snp/, 'per_snp_cluster')
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27 )
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28 """
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29 get_top_unique_mash_hit_genomes.py \\
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30 -s $sero_tbl -op $prefix
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31
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32 cat <<-END_VERSIONS > versions.yml
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33 "${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 } |
