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kkonganti@17
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1 process BCS_DISTANCE_MATRIX {
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kkonganti@17
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2 tag "Samples vs Genomes"
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kkonganti@17
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3 label "process_pico"
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kkonganti@17
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4
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kkonganti@17
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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kkonganti@17
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6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
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kkonganti@17
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@17
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8 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
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kkonganti@17
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9 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
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kkonganti@17
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10
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kkonganti@17
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11 input:
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kkonganti@17
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12 path matrix
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kkonganti@17
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13 path labels
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kkonganti@17
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14
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kkonganti@17
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15 output:
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kkonganti@17
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16 path 'bcs_sourmash_matrix.tblsum.txt', emit: mqc_txt, optional: true
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kkonganti@17
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17 path 'bcs_sourmash_matrix_mqc.json' , emit: mqc_json, optional: true
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kkonganti@17
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18 path 'bcs_sourmash_matrix_mqc.yml' , emit: mqc_yml, optional: true
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kkonganti@17
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19 path 'versions.yml' , emit: versions
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kkonganti@17
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20
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kkonganti@17
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21 when:
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kkonganti@17
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22 task.ext.when == null || task.ext.when
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kkonganti@17
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23
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kkonganti@17
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24 script:
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kkonganti@17
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25 def args = task.ext.args ?: ''
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kkonganti@17
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26
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kkonganti@17
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27 """
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kkonganti@17
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28 sourmash_sim_matrix.py \\
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kkonganti@17
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29 -pickle ${params.tuspy_ps} \\
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kkonganti@17
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30 -csv $matrix \\
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kkonganti@17
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31 -labels $labels
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kkonganti@17
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32
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kkonganti@17
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33 if [ -e "bcs_sourmash_matrix.tblsum.txt" ] && [ -s "bcs_sourmash_matrix.tblsum.txt" ]; then
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kkonganti@17
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34 create_mqc_data_table.py \\
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kkonganti@17
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35 "bcs_sourmash_matrix" \\
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kkonganti@17
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36 "The following table is an asymmetrical matrix of all <code>v.</code> all <b>ANI</b> values between each of the sample <b>FASTQ</b>'s sketch and genome <b>FASTA</b>'s sketch. Please note that there may be multiple genomes belonging to a serotype as processed by the initial screening steps of the workflow."
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kkonganti@17
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37 fi
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kkonganti@17
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38
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kkonganti@17
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39 cat <<-END_VERSIONS > versions.yml
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kkonganti@17
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40 "${task.process}":
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kkonganti@17
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41 python: \$( python --version | sed 's/Python //g' )
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kkonganti@17
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42 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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kkonganti@17
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43 END_VERSIONS
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kkonganti@17
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44 """
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kkonganti@17
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45 } |
