Description

This package contains configuration and a plugin to customize the default Illumina sample sheet generated by the SLIMS NGS execution protocol.

The package contains the following entities:

  • One plugin:
    • Illumina sample sheet generation: This plugin provides a simple way to modify the default sequencing sample sheet generated by the sample sheet step of a SLIMS NGS workflow. This plugin takes extra columns defined in a grid template and merges them into the default sample sheet.
  • One grid template:
    • Illumina sample sheet: A grid template with a context filter to fetch the samples located in the current protocol run step. This grid template contains the columns that will be included or replaced in the original sample sheet.
  • One custom field on Content:
    • 96 well Id: A field of type Short text containing a groovy script computing the sample position.

How to use the package

Pre-requisites

The MiSeq package from the Package Browser module should be installed first.

A SLIMS NGS workflow needs to be set up with one NGS execution protocol (any of the protocol types: NGS: MiSeq execution, NGS: HiSeq execution etc.).

SLIMS GATE must be running.

Configuration

  • In the Workflow Management module, in the sample sheet step of the NGS execution protocol, select the custom Illumina sample sheet plugin in the field SLIMS Gate flow generating the sample sheet by selecting “Generate sample sheet.”
  • The grid template selected in the plugin configuration can be modified. The columns defined in this grid template are merged into the default sample sheet. If the column title is present in the default sample sheet, the grid values will override the sample sheet values. However, some column titles are forbidden to use: “I7_Index_ID,” “index,” “I5_Index_ID,” and “index2.” Also, one column is required in the grid template with the title Sample_ID and field cntn_id.
  • The plugin configuration can be updated:
    • gridTemplateUniqueIdentfier: Unique identifier of the grid template that should be used by the plugin. Another grid template can be used instead of the default one.
    • removeEmptyColumns: True/false: The columns that are empty can be automatically removed when this field is set to true.

    • customSectionMap: Custom sections can be added at the top of the sample sheet using this field. For example:

      customSectionMap:
        LIMS:
          Software: "SLIMS"
          Version: "6.6.3"

      The first title below the parameter declaration corresponds to the title of the custom section. The key-value pairs below the title are copied into the sample sheet below the section title. Multiple custom sections can be added. Only default values (fixed values from the configuration) can be added.

Step by step usage

After the configuration has been done, there is no change in the execution compared to the default NGS execution steps (see Where to Look Next).

The generated sample sheet will be completed with the columns defined in the grid template and with the section defined in the customSectionMap of the plugin configuration.

Where to Look Next

These references have further information on how to configure or use the package contents after the initial installation and integration.

  • SLIMS Administration Manual:
    • Miscellaneous > Plugins Module
    • Miscellaneous > Fields > Custom Fields
    • Reporting and Grids > Grid templates
    • Workflows > Workflow Management
    • Workflows > SLIMS-NGS