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kkonganti@1
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1 process SOURMASH_COMPARE {
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kkonganti@1
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2 tag "Samples vs Genomes"
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kkonganti@1
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3 label 'process_micro'
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kkonganti@1
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
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kkonganti@1
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6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
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kkonganti@1
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7 container "${ 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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kkonganti@1
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10
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kkonganti@1
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11 input:
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kkonganti@1
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12 path queries
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kkonganti@1
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13 path accessions
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14
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kkonganti@1
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15 output:
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16 path "bcs_sourmash_cont_mat.csv" , emit: matrix, optional: true
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17 path "bcs_sourmash_cont_mat.data.labels.txt", emit: labels, optional: true
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kkonganti@1
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18 path "versions.yml" , emit: versions
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kkonganti@1
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19
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kkonganti@1
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20 when:
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kkonganti@1
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21 task.ext.when == null || task.ext.when
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22
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kkonganti@1
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23 script:
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kkonganti@1
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24 def args = task.ext.args ?: ''
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kkonganti@1
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25 def sm_compare_mode = ("${params.sourmashcompare_mode.split(',')}"
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kkonganti@1
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26 ? "--${params.sourmashcompare_mode.split(',').join(' --')}"
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kkonganti@1
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27 : '')
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kkonganti@1
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28 def sketch_args = (params.sourmashsketch_mode ?: '')
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29 sketch_args += (params.sourmashsketch_singleton ? ' --singleton ' : '')
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30 sketch_args += (params.sourmashsketch_p ? " -p ${params.sourmashsketch_p} " : '')
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kkonganti@1
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31 """
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32
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33 gen_otf_genome.py \\
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34 -gd "${params.tuspy_gd}" \\
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35 -gds "${params.tuspy_gds}" \\
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kkonganti@1
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36 -txt $accessions
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kkonganti@1
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37
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kkonganti@1
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38 if [ ! -e "CATTED_GENOMES_FAILED.txt" ]; then
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kkonganti@1
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39
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kkonganti@1
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40 sourmash sketch \\
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kkonganti@1
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41 $sketch_args \\
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42 --output OTF.db.sig \\
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kkonganti@1
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43 CATTED_GENOMES_scaffolded_genomic.fna.gz
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kkonganti@1
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44
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kkonganti@1
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45 sourmash compare \\
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kkonganti@1
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46 $sm_compare_mode \\
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kkonganti@1
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47 --${params.sourmashsketch_mode} \\
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kkonganti@1
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48 -k ${params.sourmashgather_k} \\
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kkonganti@1
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49 --csv bcs_sourmash_cont_mat.csv \\
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kkonganti@1
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50 --output bcs_sourmash_cont_mat.data \\
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kkonganti@1
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51 ${queries.collect().join(' ')} \\
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kkonganti@1
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52 OTF.db.sig
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kkonganti@1
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53 fi
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kkonganti@1
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54
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kkonganti@1
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55 cat <<-END_VERSIONS > versions.yml
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kkonganti@1
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56 "${task.process}":
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kkonganti@1
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57 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
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kkonganti@1
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58 python: \$( python --version | sed 's/Python //g' )
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kkonganti@1
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59 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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kkonganti@1
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60 END_VERSIONS
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kkonganti@1
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61 """
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kkonganti@1
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62 } |
