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Install KRAKENTOOLS_KREPORT2KRONA module
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3 changed files with 80 additions and 0 deletions
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"kraken2/kraken2": {
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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},
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"krakentools/kreport2krona": {
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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},
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"malt/run": {
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"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
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},
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36
modules/nf-core/modules/krakentools/kreport2krona/main.nf
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36
modules/nf-core/modules/krakentools/kreport2krona/main.nf
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def VERSION = '1.2' // Version information not provided by tool on CLI
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process KRAKENTOOLS_KREPORT2KRONA {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(kreport)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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kreport2krona.py \\
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-r ${kreport} \\
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-o ${prefix}.txt \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kreport2krona.py: ${VERSION}
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END_VERSIONS
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"""
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}
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41
modules/nf-core/modules/krakentools/kreport2krona/meta.yml
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modules/nf-core/modules/krakentools/kreport2krona/meta.yml
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name: krakentools_kreport2krona
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description: Takes a Kraken report file and prints out a krona-compatible TEXT file
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keywords:
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- kraken
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- krona
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- metagenomics
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- visualization
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tools:
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- krakentools:
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description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
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homepage: https://github.com/jenniferlu717/KrakenTools
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licence: ["GPL v3"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- kreport:
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type: file
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description: Kraken report
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pattern: "*.{txt,kreport}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- krona:
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type: file
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description: Krona text-based input file converted from Kraken report
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pattern: "*.{txt,krona}"
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authors:
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- "@MillironX"
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