One Case Per Sample for FASTQ

[RasmusBurge-CG]

As a user assigned to the pipeline FASTQ, I want one case per sample, So that the order-view in Trailblazer would tell me if a sample failed on amount of reads.

Acceptance Criteria

• [ ] For each sample, generate one case in any ticket that includes an app-tag related to FASTQ delivery.

...

Notes

• Additional information.
• Dependencies.
• Related user stories.

Implementation plan

• [ ] Work item 1
• [ ] Work item 2

[RasmusBurge-CG]

@karlnyr, This is a start at least

[ChrOertlin]

As a user of the trailblazer order view I would like to have FASTQ order stratified on a sample level and an indication whether samples did not reach the required amount of reads. @RasmusBurge-CG Is this right?

Added to refinement 19-06-2024

[islean]

As a user of the trailblazer order view I would like to have FASTQ order stratified on a sample level and an indication whether samples did not reach the required amount of reads. @RasmusBurge-CG Is this right?

Added to refinement 19-06-2024

I can just add that I would prefer having one case per sample than having the order summary logic depending on the workflow. Having one case per sample was also how I interpreted Rasmus' wishes

[RasmusBurge-CG]

As a user of the trailblazer order view I would like to have FASTQ order stratified on a sample level and an indication whether samples did not reach the required amount of reads. @RasmusBurge-CG Is this right? Added to refinement 19-06-2024

I can just add that I would prefer having one case per sample than having the order summary logic depending on the workflow. Having one case per sample was also how I interpreted Rasmus' wishes

Hi, yes @ChrOertlin, 'user of trailblazer' is a more accurate description. In my mind it does not need to be on a sample level, it could still be at case level(now that case and sample are somewhat equal, if we make the changes for Fastq).

I guess one only needs multiple samples in a case when we are running trios. Do you agree, @islean? This might be a good discussion for a larger audience.

Note: the changes are only suggested for pipeline FASTQ. (but I'm tempted to say that this would be a good change for all pipelines. However, I think that trios should be in the same case)

[ChrOertlin]

Ok, this is more of an trailblazer issue, I am transferring the issue there.

[Vince-janv]

Suggestion by devs:

When order is placed for FASTQ orders, create one case per sample

Considerations @ChrOertlin will look into these

get_cases_to_analyse should behave the same way.

Needs testing - although no change expected as it works for other cases as well. Mostly depends on how the OrderSubmitter stores the case data

get_analyses_to_upload should behave the same way.

Needs testing - although no change expected as it works for other cases as well. Mostly depends on how the OrderSubmitter stores the case data

See if file-structure on caesar remains the same.

Since fastq is a sample level file it will be formatted as ticket/sample/file just as it is now. No change expected. Will be confirmed with a test.

Finding "pair" samples when canceling them. Ask AZ if the change would cause issues for the lab

No issues, it would be an improvement.

According to AZ it can become a confusion that multiple fastq samples are stored under a single case if they have no relationship that just the order they are in. Especially, when just one sample needs to be cancelled the question could arise whether the whole order would need to be cancelled. If a sample would have it's own case this ambiguity would not exist.

According to KN this would be very nice!