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chore: install Bracken module
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3 changed files with 94 additions and 0 deletions
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@ -21,6 +21,10 @@
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"bracken/bracken": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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45
modules/nf-core/bracken/bracken/main.nf
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45
modules/nf-core/bracken/bracken/main.nf
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process BRACKEN_BRACKEN {
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tag "$meta.id"
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label 'process_low'
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
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'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
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input:
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tuple val(meta), path(kraken_report)
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path database
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output:
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tuple val(meta), path(bracken_report), emit: reports
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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 threshold = meta.threshold ?: 10
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def taxonomic_level = meta.taxonomic_level ?: 'S'
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def read_length = meta.read_length ?: 150
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def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
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def prefix = task.ext.prefix ?: "${meta.id}"
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bracken_report = "${prefix}_${taxonomic_level}.tsv"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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"""
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bracken \\
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${args} \\
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-d '${database}' \\
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-i '${kraken_report}' \\
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-o '${bracken_report}'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bracken: ${VERSION}
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END_VERSIONS
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"""
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}
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45
modules/nf-core/bracken/bracken/meta.yml
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modules/nf-core/bracken/bracken/meta.yml
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name: bracken_bracken
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description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
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keywords:
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- sort
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tools:
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- bracken:
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description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
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homepage: https://ccb.jhu.edu/software/bracken/
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documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
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tool_dev_url: https://github.com/jenniferlu717/Bracken
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doi: "10.7717/peerj-cs.104"
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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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- kraken_report:
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type: file
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description: TSV file with six columns coming from kraken2 output
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pattern: "*.{tsv}"
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- database:
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type: file
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description: Directory containing the kraken2/Bracken files for analysis
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pattern: "*"
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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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- reports:
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type: file
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description: TSV output report of the re-estimated abundances
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pattern: "*.{tsv}"
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authors:
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- "@Midnighter"
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