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kkonganti@101
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1 process KRAKEN2_EXTRACT_CONTIGS {
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kkonganti@101
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2 tag "$meta.id"
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kkonganti@101
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3 label 'process_nano'
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kkonganti@101
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4
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kkonganti@101
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5 module (params.enable_module ? "${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@101
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8 '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
|
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(assembly), path(kraken2_output)
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kkonganti@101
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13 val kraken2_extract_bug
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kkonganti@101
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14
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kkonganti@101
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15 output:
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kkonganti@101
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16 tuple val(meta), path('*assembly_filtered_contigs.fasta'), emit: asm_filtered_contigs
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kkonganti@101
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17 path "versions.yml" , emit: versions
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kkonganti@101
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18
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kkonganti@101
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19 when:
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kkonganti@101
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20 task.ext.when == null || task.ext.when
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kkonganti@101
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21
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kkonganti@101
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22 script:
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kkonganti@101
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23 def args = task.ext.args ?: ''
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kkonganti@101
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24 def prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@101
|
25 """
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kkonganti@101
|
26 extract_assembled_filtered_contigs.py \\
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kkonganti@101
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27 -i $assembly \\
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kkonganti@101
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28 -o ${prefix}.assembly_filtered_contigs.fasta \\
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kkonganti@101
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29 -k $kraken2_output \\
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kkonganti@101
|
30 -b '$kraken2_extract_bug'
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kkonganti@101
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31
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kkonganti@101
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32 cat <<-END_VERSIONS > versions.yml
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kkonganti@101
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33 "${task.process}":
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kkonganti@101
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34 python: \$( python --version | sed 's/Python //g' )
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kkonganti@101
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35 biopython: \$( python -c 'import Bio as bio; print(bio.__version__)' )
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kkonganti@101
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36 numpy: \$( python -c 'import numpy as np; print(np.__version__)' )
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kkonganti@101
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37 pandas: \$( python -c 'import pandas as pd; print(pd.__version__)' )
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kkonganti@101
|
38 END_VERSIONS
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kkonganti@101
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39 """
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|
kkonganti@101
|
40 } |
