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1 process OTF_GENOME {
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2 tag "$meta.id"
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3 label "process_nano"
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4
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5 module (params.enable_module ? "${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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
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9 'quay.io/biocontainers/python:3.10.4' }"
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10
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11 input:
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12 tuple val(meta), path(kma_hits), path(kma_fragz)
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13
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14 output:
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15 tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true
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16 tuple val(meta), path('*_aln_reads.fna.gz') , emit: reads_extracted, optional: true
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17 path '*FAILED.txt' , emit: failed, optional: true
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18 path 'versions.yml' , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 args += (kma_hits ? " -txt ${kma_hits}" : '')
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27 args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '')
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28 args += (prefix ? " -op ${prefix}" : '')
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29
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30 """
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31 gen_otf_genome.py \\
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32 $args
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33
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34 cat <<-END_VERSIONS > versions.yml
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35 "${task.process}":
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36 python: \$( python --version | sed 's/Python //g' )
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37 END_VERSIONS
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38 """
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39 } |
