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Clinical-Genomics / trailblazer

Keep track of and manage analyses
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One Case Per Sample for FASTQ #455

Open RasmusBurge-CG opened 2 weeks ago

RasmusBurge-CG commented 2 weeks ago

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

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Notes

Implementation plan

RasmusBurge-CG commented 2 weeks ago

@karlnyr, This is a start at least

ChrOertlin commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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