README.md

CSV Parser

To parse a CSV file with a header line:

• Define a list of fields required from the header
• In methods.config, include the csv_parser.config file and call csv_parser.parse_csv(</path/to/csv>, <fields>)

The function returns a List of Maps, where each Map corresponds to the values extracted for the requested fields for a single line in the CSV.

Available functions

• parse_csv - Function for parsing a CSV file
  • Positional args:

    position	name	type	required	default	description
    1	csv_file	String	Yes	none	String representing path to CSV file for parsing
    2	fields	List	Yes	none	List of fields to parse from CSV file

Example

To load a a CSV file defined at params.input_csv = /hot/path/to/my.csv, containing the columns patient, sample, path:

includeConfig "/path/to/csv_parser.config"
...
methods {
    ...
    def fields = ['patient', 'sample', 'path']
    parsed_inputs = csv_parser.parse_csv(params.input_csv, fields)
}