NovaSeq X integration

[Karl-Svard]

Lims Issue

Steps that need to be perfomed

• Create new sequencing steps to be used by completely new workflows.
• Update prep workflows: Decouple NovaSeq v3 and Delivery protocols from all workflows that currently use them, by creating new workflow versions.
• Set up new flow of samples between the newly created workflows by adding Queue sample automation
• Create new EPPs for: creating sample sheet v2 files used for setting up sequencing runs, and parsing data from run output files.
• Verify and validate all changes.

Progress

New workflows for validation:

Workflow	Protocol	Created in Stage	Tested in Stage	Created in Production	Tested in Production	Link to verification/initial testing issue	Link to validation report
NovaSeq X v1	NovaSeq X v1	2023-06-12 KSV	2023-08-18 KSV, IL, ARW	2023-08-23 KSV	2023-08-24 AZ, EDER	#390	#111
NovaSeq X v1	Delivery v1	2023-05-02 KSV	2023-08-18 KSV	2023-08-23 KSV	2023-08-24 AZ, EDER	#390	#111
NovaSeq 6000 v1	NovaSeq v3	2023-05-02 KSV	2023-08-18 KSV	2023-06-30 IL	2023-09-05 KSV	#391	NA
NovaSeq 6000 v1	Delivery v1	2023-05-02 KSV	2023-08-18 KSV	2023-06-30 IL	2023-09-05 KSV	#391	NA
Queue Samples for Sequencing v2	Queue Samples for Sequencing	2023-05-02 KSV	2023-06-29 ARW	2023-08-23 KSV	2023-08-23	#389, #420 - verification of new version of the validated workflow	Queue samples for sequencing Validation report

New steps

NovaSeq X v1 / NovaSeq X

• Define Run Format and Calculate Volumes (NovaSeq X)
• Make Pool and Denature (NovaSeq X)
• Prepare for Sequencing (NovaSeq X)
• NovaSeq X Run
• Bcl Conversion & Demultiplexing (NovaSeq X)
• Sequence Aggregation

Queue Samples for Sequencing v1/ Queue Samples for Sequencing

• Queue Samples for Sequencing

New EPPs created

• create_sample_sheet.py Add new Sample Sheet v2 functionalities #368 Add BarcodeMismatches support to sample sheet generation #384
• novaseq_x_volumes.py Add new EPPs for calculating NovaSeq X sequencing volumes #380
• novaseq_x_denaturation.py Add new EPPs for calculating NovaSeq X sequencing volumes #380
• pool_normalization.py Add new EPP for performing normalization of pools before sequencing #381
• xml_to_udf.py Add EPP to attach and parse sequencing xml files #385
• cg_lims/EPPs/qc/sequencing_quality_control.py Add sequencing artifact manager #407 Consume sequencing metrics endpoint #408 Add authentication token manager #412 Add sequencing quality checker #416
• ...

Modified EPPS

• move_samples.py Add new option to move-samples EPP #386

New mounts set up for NovaSeq X runs

https://github.com/Clinical-Genomics/IT-issues/issues/711

New versions of workflows for verification:

Workflow	Created in Stage	Tested in Stage	Created in Production	Tested in Production	Archive old wf	Link to verification issue
NIPT v2	2023-05-05 ARW	2023-05-17 ARW	2023-06-30 ARW	2023-09-05 IL+ARW	2023-09-08 KSV	#371
RML v7	2023-05-05 ARW	2023-05-23 ARW	2023-06-30 ARW	2023-09-05 IL+ARW	2023-09-08 KSV	#374
SARS-CoV-2 v4	2023-05-11 IL	2023-05-29 IL	2023-06-30 IL	2023-09-07 ARW	2023-09-08 KSV	#376
Microbial WGS v7	2023-05-09 ARW	2023-05-25 ARW	2023-06-30 ARW	2023-09-05 IL+ARW	2023-09-08 KSV	#372
RNA v4	2023-05-09 ARW	2023-05-31 IL	2023-06-30 IL	2023-09-05 IL+ARW	2023-09-08 KSV	#375
TWIST v8	2023-05-23 IL	2023-05-24 IL	2023-06-30 IL	2023-09-05 IL+ARW	2023-09-08 KSV	#377
WGS PCR free v6	2023-05-09 ARW	2023-05-16 ARW	2023-06-30 ARW	2023-09-05 IL+ARW	2023-09-08 KSV	#370
Development Projects v4	2023-05-11 IL	2023-05-26 ARW	2023-06-30 ARW	2023-09-05 CDM+ARW	2023-09-08 KSV	#373

Don't forget:

• Update all affected method documents
• Add new negative/positive controls for relevant steps
• Let old samples pass through before old WFs are archived
• Test a few samples through each new WF in production

Validations

...