Add a "validate" step before storage to microSALT and Mutant

[Vince-janv]

Description

Since we have no bioinformaticians willing or able to work on QC within the microSALT and Mutant code i suggest doing it in cg.

Suggested solution

To remedy the lack of QC within the microSALT and Mutant pipelines I suggest implementing a vary rudimentary "validate" method to the two analysis-apis respectively. This will be called before or within the cg workflow store command. This should in turn set the analysis as failed in trailblazer, mimicking the behaviour in the other pipelines.

This can be closed when

• [x] Mutant has a QC check - done https://github.com/Clinical-Genomics/cg/pull/3300
• [x] microSALT has a QC check - done in https://github.com/Clinical-Genomics/cg/pull/2754

Blocked by

If there are any blocking issues/prs/things in this or other repos. Please link to them.

[pbiology]

If/when this gets decided to be implemented, can we add in issues to remove these things and instead incorporate the QC checks into Clinical-Genomics/project-planning#410 and Clinical-Genomics/project-planning#23

[Vince-janv]

Decision:

• prod-bioinfo will come up with reasonable QC criteria for microSALT
• Somebody will start implementing a QC in cg for microSALT @gustavlagneborg
• @pbiology will attend a JASEN development meeting to get a feel for the status of the pipeline.
• @beatrizsavinhas Will investigate appropriate QC thresholds for Mutant
• @sofstam Will look inte the feasibility of implementing QC in Mutant instead of cg

[pbiology]

So JASEN is very closed to release. The latest status updates (22-12-01) basically says that it should happen during December 2022. Adding some module for QC also should be very possible going forward.

Once a stable version is released we should look into proper replacement of mircroSALT with JASEN, making sure that it can function as a 1:1 replacement etc. So pretty much making sure we get project Clinical-Genomics/project-planning#23 back on track