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76 lines
2.1 KiB
YAML
76 lines
2.1 KiB
YAML
name: kraken2_kraken2
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description: Classifies metagenomic sequence data
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keywords:
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- classify
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- metagenomics
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- fastq
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- db
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tools:
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- kraken2:
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description: |
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Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to sequence reads
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homepage: https://ccb.jhu.edu/software/kraken2/
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documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
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doi: 10.1186/s13059-019-1891-0
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licence: ["MIT"]
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- db:
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type: directory
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description: Kraken2 database
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- save_output_fastqs:
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type: boolean
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description: |
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If true, optional commands are added to save classified and unclassified reads
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as fastq files
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- save_reads_assignment:
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type: boolean
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description: |
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If true, an optional command is added to save a file reporting the taxonomic
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classification of each input read
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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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- classified_reads_fastq:
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type: file
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description: |
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Reads classified as belonging to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- unclassified_reads_fastq:
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type: file
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description: |
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Reads not classified to any of the taxa
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on the Kraken2 database.
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pattern: "*{fastq.gz}"
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- classified_reads_assignment:
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type: file
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description: |
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Kraken2 output file indicating the taxonomic assignment of
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each input read
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- report:
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type: file
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description: |
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Kraken2 report containing stats about classified
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and not classifed reads.
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pattern: "*.{report.txt}"
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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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authors:
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- "@joseespinosa"
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- "@drpatelh"
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