name: "sourmash_gather"
description: Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome.
keywords:
  - FracMinHash sketch
  - signature
  - kmer
  - containment
  - sourmash
  - genomics
  - metagenomics
  - taxonomic classification
  - taxonomic profiling
tools:
  - "sourmash":
      description: Compute and compare FracMinHash signatures for DNA data sets.
      homepage: https://sourmash.readthedocs.io/
      documentation: https://sourmash.readthedocs.io/
      tool_dev_url: https://github.com/sourmash-bio/sourmash
      doi: "10.21105/joss.00027"
      licence: ["BSD-3-clause"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - signature:
      type: file
      description: File containing signatures (hash sketches) of a sample
      pattern: "*.{sig}"
  - db:
      type: file
      description: Sourmash database (a list of signatures, SBTs, or signature zip files)
  - save_unassigned:
      type: boolean
      description: |
        If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query
  - save_matches_sig:
      type: boolean
      description: |
        If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query
  - save_prefetch:
      type: boolean
      description: |
        If true, output will contain a file with all prefetch-matched signatures from the database
  - save_prefetch_csv:
      type: boolean
      description: |
        If true, output will contain a csv file with the names of all prefetch-matched signatures
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - result:
      type: file
      description: |
        Table with signatures classified as belonging to any of the genomes
        in the sourmash database(s).
      pattern: "*{csv.gz}"
  - matches:
      type: file
      description: |
        A signature containing FracMinHash sketches of genomes
        in the sourmash database.
      pattern: "*{sig.zip}"
  - unassigned:
      type: file
      description: |
        A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes
        in the sourmash database(s).
      pattern: "*{sig.zip}"
  - prefetch:
      type: file
      description: |
        All prefetch-matched signatures from the database.
      pattern: "*{sig.zip}"
  - prefetchcsv:
      type: file
      description: |
        The names of all prefetch-matched signatures from the database in CSV format.
      pattern: "*{csv.gz}"
authors:
  - "@vmikk"
  - "@taylorreiter"
maintainers:
  - "@vmikk"
  - "@taylorreiter"
