Sequence Run view - too many workflows linked

[reisingerf]

It looks like the linking of workflows to a sequencing run is wrong, at least for ongoing sequence runs.

[reisingerf]

Something similar seems to happen in other circumstances.
Note: the counters in the summary bar on top don't seem to add up.

[reisingerf]

@raylrui there are more issues with the workflow linking.

As far as I understand, at the moment we can only link workflows by libraries. This creates issues when the same library was sequenced on different sequence runs. Therefore the related workflows would be listed under both sequence runs.
This is particularly confusing for "Failed" runs that have been resequenced, as the failed runs should not have any workflows associated, but still show the ones from the rerun.

A slightly better approach would be to link via fastq read sets from the FastqManager, which has a record of the originating sequence run (via instrument run id). We'd then also need to try and link those to the workflows that had those read sets as input, which is not straight forward right now. It would also not include secondary analysis workflows that don't have fastqs as input...

At this point, I'd suggest to remove / hide the workflow list in the sequence detail view and re-evaluate at a later stage.

There could also be another option to list workflows related to a sequence run: simply by date
So, instead of a dedicated workflow list in the sequence view, we could add a shortcut linking to the workflow list with a predefined date range, say sequencing success time + 2 days.
E.g.: https://orcaui.umccr.org/runs/workflow?startDate=2025-03-30T00%3A00%3A00%2B00%3A00&endDate=2025-04-01T00%3A00%3A00%2B00%3A00

That's not accurate either and will show workflows from sequencing that's happened in parallel, but it could be an easy approximation and convenience method.

[raylrui]

Thanks for the detailed explanation.

yes, the linking workflows via libraries is currently quite limiting, especially in cases where the same library appears across multiple sequencing runs.

The idea of offering a date-based shortcut of linked workflows like sequencing success time + 2 days seems still not perfect, but helpful for quick access and general context. I will implement that for temporary purpose.

Linking via fastq read sets from the FastqManager is great in the long term, even though, as you mentioned, it’s not straightforward and doesn’t cover secondary analysis workflows. I will do some research and keep it in mind for future improvements.

[reisingerf]

The quick date-based linking of workflows might be a good convenience solution. It's useful for most cases and should be easy to do.

I would shelve a longer term solution as there are a few developments that might help there. One is the warehouse, which may have better capabilities to link things together. The other one is the "case" concept, as that would link primary and secondary/tertiary workflows together.

However, even with these developments in place the fundamental issue remains that our current thinking of workflows coming from a sequencing run is a one-to-many view, where in reality it is a many-to-many relationship.

I think a better approach is to think about workflows being related to one or more data assets (usually starting from FASTQ pairs) and those assets come from one or more origins (may be sequence runs or not).
And that's not a relationship we'd want to show in a "sequence" view...