Custom Workflow

Autolaunch requires additional BaseSpace Sequence Hub and sample sheet settings.

BaseSpace Sequence Hub Requirements for ICA Autolaunch

Autolaunch uses the BaseSpace Sequence Hub (BSSH) run planning tool to create and export a v2 format sample sheet to enable streaming of sequencing run data to the project and requires the following additional settings. See Figure 1 below.

• Access to BaseSpace Sequence Hub.

• ICA Run Storage is enabled under BaseSpace Sequence Hub settings.

Refer to the BaseSpace Sequence Hub support site page for information on setting up a BaseSpace Sequence Hub project.

Illumina Cloud Run Planning and Auto-Launch Workflow

Autolaunch requires a v2 format sample sheet with specific parameters that instruct the BSSH project to automatically initiate a pipeline analysis in ICA. Use the run planning option in BaseSpace Sequence Hub to generate the sample sheet. The exported sample sheet is automatically populated with the required fields. Using an invalid sample sheet can result in failed runs and analyses.

Refer to Table 1 below for descriptions of the added fields. Enter the following required run parameters in BaseSpace Sequence Hub Run Planning:

Parameter Name	Setting
Secondary Analysis	BaseSpace Sequence Hub / Illumina Connected Analytics
Application	DRAGEN App for Whole-genome Sequencing

For more information on run planning, refer to the the run planning section

Figure 1. BSSH Run Planning Enabled End to End Workflow

BSSH enabled workflow

The BaseSpace Sequence Hub setting for run monitoring and storage must be selected on the instrument to use pipeline Analysis Software analysis Autolaunch. For information on preparing your instrument for DRAGEN App for Whole-Genome Sequencing Analysis Software Autolaunch, refer to the documentation for your instrument.

1. Use Run Planning in BaseSpace Sequence Hub to create and export a sample sheet.

2. Import the sample sheet to the instrument and start the sequencing run. Data is uploaded to BaseSpace Sequence Hub and then pushed to ICA. You can monitor the run in BaseSpace Sequence Hub.

3. When sequencing and the upload completes, analysis autolaunches in ICA. You can monitor the status of the analysis in BaseSpace Sequence Hub or ICA

4. If necessary, requeue the analysis via the run's Summary page in BaseSpace Sequence Hub. Refer to the BaseSpace Sequence Hub support site page for more information on requeuing an analysis.

5. View the analysis output results in either BaseSpace Sequence Hub or ICA.

Table 1. Additional Sample Sheet Fields for Autolaunch

Autolaunch-compatible sample sheets contain the following fields specific to autolaunch configuration.

Section	Parameter	Details	Required
Cloud_TN_Data	Sample_ID	The unique ID to identify a sample. Must match a Sample_ID used in the TN_Data section.	Yes
	Sample_Type	Sample type.	No
	Sample_Description	Must meet the following requirements:	No
		- 1–70 characters.
		- Alpha numeric characters with underscores, No dashes and spaces. If you enter an underscore, dash, or space, enter an alphanumeric character before and after.
Cloud_TN_Settings	SoftwareVersion	The software version	No
	StartsFromFastq	Set the value to TRUE or FALSE. If autolaunching from BCL files, this must be set to FALSE.	Yes
Cloud_Data	Sample_ID	The same sample ID used in the Cloud_TN_Data section.	No
	ProjectName	The BaseSpace Sequence Hub project name.	No
	LibraryName	Combination of sample ID and index values in the No following format: sampleID_Index_Index2.	No
	LibraryPrepKitName	The Library Prep Kit used.	No
	IndexAdapterKitName	The Index Adapter Kit used.	No
Cloud_Settings	GeneratedVersion	The cloud GSS version used to create the sample sheet. Optional if manually updating a sample sheet.	No
	CloudWorkflow	ica_workflow_1	Yes
	Cloud_TN_Pipeline	This value is a universal record number (URN). The valid value is defined in Quick Start	Yes