Process Summary Report

Available from: Clarity LIMS v2.0.5

Often, a user wants to determine what work has been performed on several samples by running the Sample History Report. However, suppose they were to use the sampleHistoryReport script on 600 samples that involve the same four processes. The result would be 600 reports (one for each sample), each of which provides information on only that one sample.

A preferable alternative is to use the processHistoryReport script, which is run only once for each process. In this example, therefore, it would produce only four reports (one for each process) allowing for a better grouping of information and less files.

Script Overview

The processHistoryReport script has two parts: 1. Retrieve the necessary information, and 2. Compile that information into a report.

• The script generates one report ('Process Summary Report') for all inputs, output as a single shared result file.

• The script is configured on the Illumina Sequencing (Illumina SBS) 5.0 step, as 'Report creation script.'

• The report is generated in XLS format using POI.

• The report is automatically attached to the pre-configured report process result file output.

Script Parameters

Adding Processes to a Report

1. Add a process UDF of type Checkbox, with the exact name of the process you want to include. For example: "3. Denature, Dilute and Load Sample (MiSeq)"

2. When the process is run, select the checkbox to include that process in the Process Summary Report.

   Copy

   OUTPUT GENERATION NAMING EXAMPLE:
   Process History Report
   
   EPP PARAMETER STRING EXAMPLE:
   java -jar ngs-extensions.jar script:processHistoryReport -u {username} -p {password} -i {processURI}

Note that the script may also be run in the following directory:

/opt/gls/clarity/extensions/ngs-common/v5/EPP

Configuration

Report process configuration may be obtained using the LIMS configuration import/export tools or the LIMS Config-Slicer tool.

Rules & constraints

• The script must be run from the LIMS Operations Interface.

• To be included in the report, a process must have at least one output UDF specified.

• The report requires a pre-configured process type + EPP parameter string ('TruSeq Process Summary Report').

• The report runs from the specified artifact down the genealogy tree. For complete and correct output, it is recommended that it be run on the original submitted samples.

Additional information

Other scripts you may find useful:

• Set UDF

• Copy UDFs