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1 process SOURMASH_GATHER {
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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(signature), path(database)
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13 val save_unassigned
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14 val save_matches_sig
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15 val save_prefetch
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16 val save_prefetch_csv
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17
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18 output:
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19 tuple val(meta), path("*.csv.gz") , emit: result , optional: true
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20 tuple val(meta), path("*_scaffolded_genomic.fna.gz"), emit: genomes_fasta, optional: true
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21 tuple val(meta), path("*_unassigned.sig.zip") , emit: unassigned , optional: true
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22 tuple val(meta), path("*_matches.sig.zip") , emit: matches , optional: true
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23 tuple val(meta), path("*_prefetch.sig.zip") , emit: prefetch , optional: true
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24 tuple val(meta), path("*_prefetch.csv.gz") , emit: prefetchcsv , optional: true
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25 path "*FAILED.txt" , emit: failed , optional: true
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26 path "versions.yml" , emit: versions
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27
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28 when:
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29 task.ext.when == null || task.ext.when
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30
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31 script:
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32 def args = task.ext.args ?: ''
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33 def args2 = task.ext.args2 ?: ''
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34 def prefix = task.ext.prefix ?: "${meta.id}"
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35 def unassigned = save_unassigned ? "--output-unassigned ${prefix}_unassigned.sig.zip" : ''
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36 def matches = save_matches_sig ? "--save-matches ${prefix}_matches.sig.zip" : ''
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37 def prefetch = save_prefetch ? "--save-prefetch ${prefix}_prefetch.sig.zip" : ''
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38 def prefetchcsv = save_prefetch_csv ? "--save-prefetch-csv ${prefix}_prefetch.csv.gz" : ''
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39 def gd = params.tuspy_gd ? "-gd ${params.tuspy_gd}" : ''
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40
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41 """
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42 sourmash gather \\
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43 $args \\
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44 --output ${prefix}.csv.gz \\
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45 ${unassigned} \\
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46 ${matches} \\
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47 ${prefetch} \\
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48 ${prefetchcsv} \\
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49 ${signature} \\
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50 ${database}
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51
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52 sourmash_filter_hits.py \\
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53 $args2 \\
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54 -csv ${prefix}.csv.gz
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55
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56 gen_otf_genome.py \\
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57 $gd \\
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58 -op ${prefix} \\
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59 -txt ${prefix}_template_hits.txt
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60
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61 cat <<-END_VERSIONS > versions.yml
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62 "${task.process}":
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63 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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64 python: \$( python --version | sed 's/Python //g' )
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65 END_VERSIONS
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66 """
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67 } |
