---
files:
  #' The pattern identifying your whole job. You can put whatever you want. STRING
  pattern: example
  features:
    #' The path to the file containing your features' intensities.
    #' Can be generated by MZMine3 or SLAW. STRING
    raw: data/source/example_features.csv
  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
  spectral:
    #' The path to the file containing your features' spectra.
    #' Can contain MS1 and/or MS2 spectra. STRING
    raw: data/source/example_spectra.mgf
  #' Annotations files.
  annotations:
    raw:
      #' Directory containing the sirius annotations. STRING
      sirius: data/interim/annotations/example_sirius.zip
ms:
  #' The polarity used. Must be either "pos" or "neg". STRING
  polarity: pos
organisms:
  #' 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: ~
options:
  #' Filter high confidence candidates only. BOOLEAN
  high_confidence: yes
  #' Do you want to summarize all candidates per feature to a single row? BOOLEAN
  summarise: no
