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1 process SEQSERO2 {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null)
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6 conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' :
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9 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }"
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10
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11 input:
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12 tuple val(meta), path(reads_or_asm)
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13
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14 output:
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15 path("${meta.id}${params.fs}*")
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16 tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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25 """
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26 SeqSero2_package.py \\
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27 $args \\
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28 -d $prefix \\
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29 -n $prefix \\
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30 -p $task.cpus \\
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31 -i $reads_or_asm
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32
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33 mv ${prefix}${params.fs}SeqSero_log.txt ${prefix}${params.fs}${prefix}.SeqSero_log.txt
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34 mv ${prefix}${params.fs}SeqSero_result.txt ${prefix}${params.fs}${prefix}.SeqSero_result.txt
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35 mv ${prefix}${params.fs}SeqSero_result.tsv ${prefix}${params.fs}${prefix}.SeqSero_result.tsv
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36
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37 cat <<-END_VERSIONS > versions.yml
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38 "${task.process}":
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39 seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
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40 END_VERSIONS
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41 """
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42 } |
