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0
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1 process RMLST_POST {
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2 tag "${meta.id}"
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3 label "process_pico"
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4 maxForks 3
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5
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6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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7 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null)
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8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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9 'https://depot.galaxyproject.org/singularity/requests:2.26.0' :
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10 'quay.io/biocontainers/requests:2.26.0' }"
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11
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12 input:
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13 tuple val(meta), path(genome)
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14
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15 output:
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16 tuple val(meta), path('*.tsv') , emit: tsv, optional: true
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17 tuple val(meta), path('*.log.json'), emit: log, optional: true
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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 prefix = (task.ext.prefix ?: meta.id)
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25
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26 """
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27 rmlst_post.py \\
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28 -fasta $genome \\
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29 -prefix $prefix \\
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 python: \$( python --version | sed 's/Python //g' )
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34 requests: \$( python -c "import requests; print (requests.__version__)" )
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35 END_VERSIONS
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36 """
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37 } |
