Requirements
The TN pipeline has fields that are required in addition to general sample sheet requirements. Follow the steps below to create a valid samplesheet.
Standard Sample Sheet Requirements
The following sample sheet requirements describe required and optional fields for TN pipeline. Depending on the deployment (standalone DRAGEN server, ICA with auto-launch, ICA with manual launch), certain sections and required values can deviate from the standard requirements. These deviations are noted in the information below.
The analysis fails if the sample sheet requirements are not met.
Use the following steps to create a valid sample sheet.
Download the sample sheet v2 template that matches the instrument & assay run.
In the Sequencing Settings section, enter the following required parameters:
[Sequencing_Settings] Section
LibraryPrepKits
Required
Accepted values are: IlluminaDNAPrep or IlluminaDNAPCRFree
In the BCL Convert Settings section, enter the following required parameters:
[BCLConvert_Settings] Section
SoftwareVersion
Required
The DRAGEN component software version. The TN pipeline requires 4.4.4 or higher. To ensure you are using the latest compatible version, refer to the software release notes.
AdapterRead1
Required
If using 10 bp indexes with UDP: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC Analysis fails if the incorrect adapter sequences are used
AdapterRead2
Required
If using 10 bp indexes with UDP: CTGTCTCTTATACACATCTGACGCTGCCGACGA Analysis fails if the incorrect adapter sequences are used
AdapterBehavior
Optional
Enter trim This indicates that the BCL Convert software trims the specified adapter sequences from each read.
MinimumTrimmedReadLength
Optional
Enter 35. Reads with a length trimmed below this point are masked.
MaskShortReads
Optional
Enter 35. Reads with a length trimmed below this point are masked.
In the BCL Convert Data section, enter the following parameters for each sample.
[BCLConvert_Data] Section
Sample_ID
Required
Must match a Sample_ID listed in the [TN_Data] section section.
Index
Required
Index 1 sequence valid for Index_ID assigned to matching Sample_ID in the [TN_Data] section.
Index2
Required
Index 2 sequence valid for Index_ID assigned to matching Sample_ID in the [TN_Data] section.
Lane
Only for NovaSeq 6000 XP, NovaSeq 6000Dx, or NovaSeq X workflows
Indicates which lane corresponds to a given sample. Enter a single numeric value per row. Cannot be empty, i.e the analysis fails if the Lane column is present without a value in each row.
In the [TN_Data] section, enter the following parameters:
[TN_Data] Section header changes depending on the deployment: Section header changes depending on the deployment:
Standalone DRAGEN Server and ICA with Manual Launch:
TN_DataICA with Auto-launch:
Cloud_TN_Data
[TN_Data] Section
Sample_ID
Required
The unique ID to identify a sample. The sample ID is included in the output file names. Sample IDs are not case sensitive. Sample IDs must have the following characteristics:
- Unique for the run.
- 1–70 characters.
- No spaces.
- Alphanumeric characters with underscores and dashes. If you use an underscore or dash, enter an alphanumeric character before and after the underscore or dash. eg, Sample1-T5B1_022515.
- Cannot be called all, default, none, unknown, undetermined, stats, or reports.
- Must match a Sample_ID listed in the [BCLConvert_Data] section. Each sample must have a unique combination of Lane (if applicable), sample ID, and index ID or the analysis will fail.
Sample_Type
Optional
Enter DNA
Case_ID
Optional
A unique ID that links the same biological samples from the same individual. It is used for variant interpretation in downstream software such as the Illumina Connected Insights software
Sample_Description
Optional
Sample description must meet the following requirements: - 1–50 characters. - Alphanumeric characters with underscores, dashes and spaces. If you enter a underscore, dash, or space, enter an alphanumeric character before and after. eg, Solid-WGS_213.
To ensure a successful analysis, follow these guidelines:
Avoid any blank lines at the end of the sample sheet; these can cause the analysis to fail.
When running local analysis using the command line save the sample sheet in the sequencing run folder with the default name
SampleSheet.csv, or choose a different name and specify the path in the command-line options.
ICA with Auto-launch: Sample Sheet Requirements
To auto-launch analysis from the sequencer run folder, ensure the StartsFromFastq and SampleSheetRequested fields are set to FALSE. To auto-launch analysis from FASTQs after BCL Convert auto-launch, StartsFromFastq and SampleSheet Requested fields must be set to TRUE
[Cloud_TN_Data] Section
[Cloud_TN_Settings] Section
SoftwareVersion
Not Required
The TN pipeline software version
StartsFromFastq
Required
Set the value to TRUE or FALSE. To auto-launch from BCL files, set to FALSE. To auto-launch from FASTQ files after auto-launch of BCL Convert, set to TRUE.
SampleSheetRequested
Required
Set the value to TRUE or FALSE. To auto-launch from BCL files, set to FALSE. To auto-launch from FASTQ files after auto-launch of BCL Convert, set to TRUE.
[Cloud_Data] Section
Sample_ID
Not Required
The same sample ID used in the Cloud_TNS_Data section.
ProjectName
Not Required
The BaseSpace project name.
LibraryName
Not Required
Combination of sample ID and index values in the following format: sampleID_Index_Index2
LibraryPrepKitName
Required
The Library Prep Kit used.
IndexAdapterKitName
Not Required
The Index Adapter Kit used.
[Cloud_Settings] Section
GeneratedVersion
Not Required
The cloud GSS version used to create the sample sheet. Optional if manually updating a sample sheet.
CloudWorkflow
Not Required
Ica_workflow_1
Cloud_TN_Pipeline
Required
This value is a universal record number (URN). The valid values are: [TODO] add pipeline IDs
BCLConvert_Pipeline
Required
The value is a URN in the following format: urn:ilmn:ica:pipeline: <pipeline-ID>#<pipeline-name>
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