---
#' Files.
files:
  #' Annotations files.
  annotations:
    #' Raw annotations files.
    raw:
      #' Directory containing the sirius annotations. STRING
      sirius: data/interim/annotations/example_sirius

    #' List of prepared annotations.
    prepared:
      #' List of prepared canopus annotations. STRING
      canopus: data/interim/annotations/example_canopusPrepared.tsv.gz

      #' List of prepared formula annotations. STRING
      formula: data/interim/annotations/example_formulaPrepared.tsv.gz

      #' List of prepared structural annotations.
      structural:
        #' Prepared SIRIUS structural annotations. STRING
        sirius: data/interim/annotations/example_siriusPrepared.tsv.gz

  #' Libraries files.
  libraries:
    #' Structure organism pairs libraries.
    sop:
      #' Merged structure organism pairs library.
      merged:
        #' Structures libraries.
        structures:
          #' Structures stereo. STRING
          stereo: data/interim/libraries/sop/merged/structures/stereo.tsv.gz

          #' Structures metadata. STRING
          metadata: data/interim/libraries/sop/merged/structures/metadata.tsv.gz

          #' Structures names. STRING
          names: data/interim/libraries/sop/merged/structures/names.tsv.gz

          #' Structures taxonomies.
          taxonomies:
            #' Classyfire structures taxonomy. STRING
            cla: data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz

            #' NPClassifier structures taxonomy. STRING
            npc: data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz

#' Tools used for each step.
tools:
  #' Sirius.
  sirius:
    #' Sirius version.
    #' Currently only 5 or 6 supported. INTEGER
    version: 6
  #' Taxonomies related parameters.
  taxonomies:
    #' Chemical taxonomy used for matching.
    #' Currently only "npc" or supported. STRING
    chemical: npc
