---
#' Files.
files:
  #' Features files.
  features:
    #' Raw features file. STRING
    raw: data/source/example_features.csv

  #' Metadata files.
  metadata:
    #' The path to the file containing your metadata.
    #' Must be formatted accordingly.
    #' If your experiment contains a single taxon, you can provide it below instead. STRING
    raw: data/source/example_metadata.tsv

    #' Taxonomically informed features file. STRING
    prepared: data/interim/taxa/example_taxed.tsv.gz

  #' Libraries files.
  libraries:
    #' Structure organism pairs libraries.
    sop:
      #' Merged structure organism pairs library.
      merged:
        #' Organisms libraries.
        organisms:
          #' Organisms taxonomies.
          taxonomies:
            #' OTT organisms taxonomy. STRING
            ott: data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz

#' Names of the different variables in the input files.
names:
  #' The file(s) extension is present in the sample name. BOOLEAN
  extension: yes

  #' Name of "feature IDs" variable in the input. STRING
  features: row ID

  #' Name of "filename" variable in the input. STRING
  filename: filename

  #' Name of the "taxon name" variable in the input. STRING
  taxon: ATTRIBUTE_species

#' Organisms related parameters.
organisms:
  #' Number of organisms to keep per feature. INTEGER
  candidates: 1

  #' OPTIONAL. If your experiment contains a single taxon, its scientific name.
  #' Else, you will need to provide a metadata file above.
  #' If you provide both, this one will have priority.
  #' Example: "Homo sapiens". STRING
  taxon: ~
