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49 lines
1.4 KiB
YAML
49 lines
1.4 KiB
YAML
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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- bracken
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- metagenomics
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- abundance
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- kraken2
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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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