Verification of new workflow version: RML v8

idalindegaard commented 1 year ago

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: RML v8 Protocol: CG002 Reception Control, CG002 RML Pool samples, CG002 RML Initial QC v3 Step:

Description:

With the new workflow setup where we have two separate sequencing workflows (NovaSeq 6000 and NovaSeq X), we need to create new versions of all workflows that end with sequencing. We will remove protocols NovaSeq v3 and Delivery v1, and include a new automation to queue the samples to an intermediate workflow, Queue samples for sequencing. Following documents New workflow in LIMS and Validation and verification, all new versions of workflows need to be verified.

The verification includes

creating the new workflow version in the LIMS stage environment
testing it with different scenarios and adding screenshots of the tests in this issue
create the workflow in the LIMS production environment
test the workflow in production

Since many protocols are straight out copied from the previous version they won't go through extensive testing, we will just check that they perform satisfactorily with regular samples.

Actions:

The new workflow is essentially the same as v6, and consists of three protocols:

CG002 Reception Control: same protocol as in RML v6 CG002 RML Pool samples: same protocol as in RML v6 CG002 RML Initial QC v3: new protocol, same as in v1, except:

removed CG002 - qPCR QC (Library Validation)
updated Aggregate QC (DNA)
- created new Automation Queue samples for sequencing (from QC step)
- added new automation to master step Aggregate QC (DNA)
- activated automation as Automatic upon exit in Record details

Protocol	Created in Stage	Tested in Stage	Created in Production
CG002 Reception Control	N/A*	Done! 2023-05-23 ARW	N/A
CG002 RML Pool samples	N/A*	Done! 2023-05-23 ARW	N/A
CG002 RML Initial QC v3	Done! 2023-05-17 ARW	Done! 2023-05-23 ARW	2023-06-12 ARW

*This protocol is the same as in the previous version of the workflow

Testing setup:

Eight samples will be run through the entire workflow. For protocols CG002 Reception Control and CG002 RML Pool samples, the samples will just be passed on through the steps to test that they perform the same as in the current workflow (v6). For protocol CG002 RML Initial QC v3, only the last step has been altered as compared to v1. This step will be verified to see that the new function of queueing samples to the workflow Queue Samples for Sequencing works.

The plate was named verrml230523

All samples were from #327440

LIMS ID (Sample)	Sample Name	Apptag
ACC11446A1	PB-P-OLVA4006-CFDNA-Ctrl1-KH20230213-C420230214	RMLP15R100
ACC11446A2	PB-P-OLVA4006-CFDNA-Ctrl2-KH20230213-C420230214	RMLP15R100
ACC11446A3	PB-P-OLVA4006-CFDNA-Ctrl3-KH20230213-C420230214	RMLP15R100
ACC11446A4	PB-P-OLVA4006-CFDNA-Wash1-KH20230213-C420230214	RMLP15R100
ACC11446A5	PB-P-OLVA4006-CFDNA-Wash2-KH20230213-C420230214	RMLP15R100
ACC11446A7	PB-P-OLVA4006-CFDNA-evaporation1-KH20230213-C420230214	RMLP15R100
ACC11446A8	PB-P-OLVA4006-CFDNA-Evaporation2-KH20230213-C420230214	RMLP15R100
ACC11446A9	PB-P-OLVA4006-CFDNA-Evaporation3-KH20230213-C420230214	RMLP15R100

Protocol	Step	Test specification	Comments/Results	P/F	Sign
CG002 Reception Control	CG002 - Reception Control	NA**	All 8 samples passed without error messages. All EPPs functional	P	2023-05-23 ARW
CG002 RML Pool samples	CG002 - RML Library Pooling	NA**	All 8 samples passed without error messages. All EPPs functional	P	2023-05-23 ARW
CG002 RML Initial QC v3	CG002 - Qubit QC RML	NA**	All 8 samples passed without error messages. All EPPs functional. Used Qubit values from original run on 230216 (320 bp, 1,78 ng/ul)	P	2023-05-23 ARW
CG002 RML Initial QC v3	CG002 - Aggregate QC (DNA)	Test using 8 samples in one pool. Check that there are no errors with EPPs. Check that samples are queued to the correct workflow	All 8 samples passed without error messages. All EPPs functional. The pool was successfully aggregated and queued to the correct workflow	P	2023-05-23 ARW

**The step is the same as in the previous version of the workflow and will not be tested specifically with different scenarios

Project resources:

Screen shots of all steps can be found on Google Drive

Conclusions:

The workflow passed the verification and is ready to be used in production.

Sign off

Head of Unit Lab	Date
ALY	2023-08-25

Implementation

What is needed to implement changes	Item	Date signature
Information to staff	1. Email sent out to email adress clinical_production@scilifelab.se 2. Inform during lab meeting 3. Inform lab staff on Slack when workflow is activated	1. 2023-08-23 IL 2. 2023-08-28 ARW + IL 3. 230829/ARW+IL
Documentation	No Atlas updates needed, no mention of protocol version in NovaSeq 6000 Sequencing method	N/A
Test in production	Monitor workflow performance during the first week after activation	2023-09-05 ARW+IL
Move negative controls	N/A	N/A
Move ongoing samples	N/A (workflow update was performed between two NIPT runs)	N/A
Archive old workflow version and hide from lab view	Archive workflow RML v7	KSV

[x] Verification completed and implemented

amandaraud commented 1 year ago

Testing in stage done! Ready to be created in production.

amandaraud commented 1 year ago

Workflow created in production (pending), ready to be activated and tested.

amandaraud commented 1 year ago

Ready to be signed off @annaengstrom

Clinical-Genomics / cg_lims