annotation_template.yaml

pattern: #  List of file patterns to match with the current annotation; required
  - string
  - string
  - ...
format: string # Output format "tsv" or "csv"; default: "tsv"
delimiter: string # Delimiter of input files: t - tabular, c - coma; default: "t"

columns: # A list of columns that we want as an output; optional (otherwise it will show all the annotation fields)
  - string
  - string
  - ...

annotation: # Columns to parse
  # Required attributes in each annotation element:
  # 'type': Describe the type of field that will be parsed.
  # Could be: static, internal, filename, dirname, mapping, plugin
  # 'field': The name of the column that will be parsed

  # The value will be parsed to all the rows of the output file
  - type: 'static'
    field: string
    value: string | number # Value that it will be written to the output file; required

  # The values of `fieldSource` columns that appears on the input files will
  # be extracted and parsed as values in the output
  - type: 'internal'
    field: string
    value: string # Text to represent multiple fieldSource; optional
    fieldSource: # Columns to look for in the input files; required
      - string
      - string
      - ...
    function: string # Function to apply to internal value; optional

  # Annotation based on the filename of the input file
  - type: 'filename'
    field: string
    function: string # Function to apply to filename; optional
    regex: string # Regular expression to apply to filename, after function; optional

  # Annotation based on the dirname that input file is located
  - type: 'dirname'
    field: string
    function: string # Function to apply to dirname; optional
    regex: string # Regular expression to apply to dirname, after function; optional

  # Mapping annotation allows to use a mapping file to add a new column base on a many-to-one relation
  - type: 'mapping'
    field: string
    fieldSource: # Fields (from annotation file) to look and map in the input file; required
      - string
      - string
      - ...
    fieldMapping: string # Field to map in the mapping file; required
    fileMapping: string # File name to make the mapping; required
    fieldValue: string # Field of the final output value; required

  # Apply plugin transformation in each row of the input file.
  - type: 'plugin'
    plugin: string # Plugin to apply, could be internal, located into 'plugin' folder, or customized by the user
    field: string

exclude: # List of field and value that allows to filter out all the rows that have specific value; optional
  - field: string # Field to apply the exclusion
    value: string # Value that will be discarded
  - ...