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79 lines
2.3 KiB
YAML
79 lines
2.3 KiB
YAML
name: "krakenuniq_preloadedkrakenuniq"
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description: Classifies metagenomic sequence data using unique k-mer counts
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keywords:
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- classify
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- metagenomics
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- kmers
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- fastq
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- db
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tools:
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- "krakenuniq":
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description: "Metagenomics classifier with unique k-mer counting for more specific results"
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homepage: https://github.com/fbreitwieser/krakenuniq
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documentation: https://github.com/fbreitwieser/krakenuniq
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doi: 10.1186/s13059-018-1568-0
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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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- fastqs:
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type: file
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description: List of input FastQ files
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- db:
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type: directory
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description: KrakenUniq database
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- ram_chunk_size:
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type: val
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description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time
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pattern: "*GB"
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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 KrakenUniq 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 KrakenUniq database.
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pattern: "*.fastq.gz"
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- classified_assignment:
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type: file
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description: |
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KrakenUniq output file indicating the taxonomic assignment of
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each input read ## DOUBLE CHECK!!
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- report:
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type: file
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description: |
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KrakenUniq 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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- "@mjamy"
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- "@Midnighter"
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