align_methods.config

/**
*   This methods namespace contains common functions for alignment pipeline input handling.
*/
align_methods {
    /**
     * Sets the parameters from the input which may be either a YAML (specified with key 'input')
     * or a CSV (specified with key 'input_csv')
     */
    set_params_from_input = {
        if (params.containsKey('input_csv')) {
            def reader = new BufferedReader(new FileReader(params.input_csv))

            header_line = reader.readLine()
            def csv_header_fields = header_line.split(',') as List
            def raw_csv_input = csv_parser.parse_csv(params.input_csv, csv_header_fields)

            // format the raw input so it matches the YAML
            params.input = ['FASTQ': []]

            // extract the inputs from the parsed csv
            def extracted_inputs = [] as Set
            raw_csv_input.each { csv_line ->
                extracted_inputs.add(
                    csv_line
                )
            }
            params.input.FASTQ = extracted_inputs
        } else if (!(params.containsKey('input'))) {
            throw new IllegalArgumentException('Neither YAML nor CSV inputs found! Please run pipeline with inputs.')
        }
    }
}