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1 process SOURMASH_SKETCH {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
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6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
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9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
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10
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11 input:
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12 tuple val(meta), path(sequence), path(database)
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13
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14 output:
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15 tuple val(meta), path("*.query.sig"), path("*.db.sig"), emit: signatures
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 // required defaults for the tool to run, but can be overridden
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23 def args = task.ext.args ?: ''
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24 def args_query
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 """
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27 sourmash sketch \\
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28 ${args.toString().replace('--singleton', '')} \\
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29 --output "${prefix}.query.pre" \\
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30 $sequence
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31
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32 sourmash signature rename \\
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33 --${args.toString().replaceAll(/\s+\-p.*/, '')} \\
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34 -o "${prefix}.query.sig" \\
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35 "${prefix}.query.pre" \\
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36 ${prefix}
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37
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38 sourmash sketch \\
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39 $args \\
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40 --output "${prefix}.db.sig" \\
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41 $database
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42
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43 cat <<-END_VERSIONS > versions.yml
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44 "${task.process}":
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45 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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46 END_VERSIONS
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47 """
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48 } |
