Getting Started - Sample Input Sheet Generator

Compatibility: NGS v5.16 and earlier

The driver_file_generator.groovy script uses a supplied template file to produce a corresponding sample input sheet file. This enables the user to produce custom sample input sheet files through the creation of an appropriate template file, without requiring scripting or development resources.

Note that while the output format of the template file is not limited to CSV, this is the most common sample sheet file format encountered.

Most CSV-based sample input sheet files follow the same basic structure: metadata, header block, header, data, footer. (For details, see Sample Input Sheet Template Sections .)

1. The script is initiated via EPP/automation.
2. The script uses a CSV template file to create a sample input sheet file, based on the specifications within the template.
3. The script then extracts data from the LIMS via the API based on tokens defined as ${TOKENTEXT} within the template. (The available tokens are described in Creating Sample Input Sheet Templates .)

A few special options are available for inclusion in the template. These do not directly pull data from the API. Instead, they modify what has been gathered in the sample sheet file. These options are outlined under the Metadata section in Sample Input Sheet Template Sections .

4. The script parses the comma-delimited template file and processes the five sections this file may contain: metadata, header block, header, data, and footer, each of which is enclosed inside tags.

For example:

<HEADER_BLOCK>Header block entry one, two, three More information </HEADER_BLOCK>

If any of the following conditions is not met - the tag, and everything inside of it, will be ignored by the script and a warning will display in the log file:

• With the exception of the metadata, all template sections must be enclosed inside tags.
• Each tag must have its own line, and must be the only tag present on that line.
• No other entries, even empty ones, are allowed.
• All opened tags must be closed.