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kkonganti@101
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1 process CENTRIFUGE_PROCESS {
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kkonganti@101
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2 tag "$meta.id"
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kkonganti@101
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3 label 'process_low'
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kkonganti@101
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4
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kkonganti@101
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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kkonganti@101
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6 conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::pandas conda-forge::biopython" : null)
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kkonganti@101
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@104
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8 'https://depot.galaxyproject.org/singularity/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' :
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kkonganti@101
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9 'quay.io/biocontainers/mulled-v2-d91be2208450c41a5198d8660b6d9a5b60613b3a:d9847b41af5ef58746c86d7114cd010650f3d9a2-0' }"
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kkonganti@101
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10
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kkonganti@101
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11 input:
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kkonganti@101
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12 tuple val(meta), path(centrifuge_report), path(centrifuge_output)
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kkonganti@101
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13
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kkonganti@101
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14 output:
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kkonganti@101
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15 tuple val(meta), path('*.process-centrifuge-bug-ids.txt'), emit: extracted
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kkonganti@101
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16 path "versions.yml" , emit: versions
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kkonganti@101
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17
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kkonganti@101
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18 when:
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kkonganti@101
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19 task.ext.when == null || task.ext.when
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kkonganti@101
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20
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kkonganti@101
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21 script:
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kkonganti@101
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22 def args = task.ext.args ?: ''
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kkonganti@101
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@101
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24 """
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kkonganti@101
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25 process_centrifuge_output.py \\
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kkonganti@101
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26 -r $centrifuge_report \\
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kkonganti@101
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27 -o $centrifuge_output \\
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kkonganti@101
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28 -b '${params.centrifuge_extract_bug}' \\
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kkonganti@101
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29 -t ${prefix}.process-centrifuge-bug-ids.txt
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kkonganti@101
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30
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kkonganti@101
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31 cat <<-END_VERSIONS > versions.yml
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kkonganti@101
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32 "${task.process}":
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kkonganti@101
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33 python: \$( python --version | sed 's/Python //g' )
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kkonganti@101
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34 biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' )
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kkonganti@101
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35 numpy: \$( python -c 'import numpy as np; print(np.__version__)' )
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kkonganti@101
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36 pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' )
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kkonganti@101
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37 END_VERSIONS
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kkonganti@101
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38 """
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kkonganti@101
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39 } |
