Create orderflow for microbial sequencing only

[Vince-janv]

Description

For human DNA samples customers can order different analysis workflow but they can also order sequencing only (FASTQ) where we just send them the FASTQ files.

This option does not exist for microbial samples where only a microSALT analyses are available and require input parameters which the customers might not have.

Acceptance Criteria

• [ ] Customers can order sequencing for microbial samples without further analyses
• [ ] The FASTQ files are automatically uploaded once sequencing is done

Notes

• We need input on which input fields are needed for the lab when ordering @annagellerbring
• Should ideally create on case per sample IMO

Implementation plan

• ...

[ChrOertlin]

@Vince-janv does this issue need a technical refinement? If not we should add it to the trocadero "ready" column. Otherwise we have to add it to the refinement meeting.

[Vince-janv]

@Vince-janv does this issue need a technical refinement? If not we should add it to the trocadero "ready" column. Otherwise we have to add it to the refinement meeting.

I will call relevant people to refinement and put it in the ready column when finished

[annagellerbring]

Lab UDFs in new workflow: (in discussion with @FayKanellidou)

Keep:

• Sample/Name
• UDF/Control
• UDF/Sequencing Analysis (Application tag)
• UDF/customer
• UDF/Sample Buffer
• UDF/Volume
• UDF/Priority
• Container/Tube (Container Type)
• Container/Name (Plate Name)
• Sample/Well location (Well)
• UDF/Comment

Remove:

• UDF/Extraction method
• UDF/Sample conc.
• UDF/Quantity

FYI @annaengstrom @AnnaZetterlund

[Vince-janv]

Technical Refinement

FE

• Add new "orderType" to the front end called Sequencing of microbial samples
  • text: "Sequencing of microbial samples"
  • orderType: microbial-fastq
  • applications:[mic, cov]
  • dataAnalysis: fastq
• deliveryOptions: [fastq: { text: 'Raw sequencing data (fastq)', value: 'fastq' }, no_delivery: { text: 'No Delivery', value: 'no-delivery' },]
• The fields should be those described in AGs comment

BE

• Allow for new ordertype in submit-endpoint https://github.com/Clinical-Genomics/cg/pull/3701
• New OrderInSample child class called MicrobialFastqSample https://github.com/Clinical-Genomics/cg/pull/3553
• Add new MicrobialFastqSubmitter (avoid MicrobialSubmitter....) https://github.com/Clinical-Genomics/cg/pull/3701
• The Case database object should have case.data_analysis="fastq" and case.data_delivery="fastq" https://github.com/Clinical-Genomics/cg/pull/3701

[ChrOertlin]

Backend solutions are in place now. Waiting on FE implementaiton to test.

[ChrOertlin]

@Vince-janv What are the fields that need to be displayed on the front end. @moedarrah and I are testing and we run into issues with validation errors when fields become hidden on the fornt end.

For example when putting no container then the volume disappears which is required when putting a microbial fastq order

[moedarrah]

An error will occur if we don't specify the "Volume (μL)", which will be hidden when "No Container" is selected.

[diitaz93]

@Vince-janv

[Vince-janv]

@Vince-janv What are the fields that need to be displayed on the front end. @moedarrah and I are testing and we run into issues with validation errors when fields become hidden on the fornt end.

For example when putting no container then the volume disappears which is required when putting a microbial fastq order

@moedarrah Was Volume the only field? I looked into it and the same bug is present for the exists in the current microbial workflow in production. I'm in contact with prod whether to disallow No container for both or allow it for both (and fix the bug)

[Vince-janv]

After discussion with KN we decided that for both the existing microbial flow and for this one, the option No-container should not be available. @moedarrah Not sure what the best way to implement this is. If it is a hassle in the front-end we can sit down and refine it a bit

[moedarrah]

@Vince-janv For the front end, there is no issue. We just need to ensure that the backend accepts the order without requiring the 'Volume (μL)' field.

[Vince-janv]

@moedarrah It's rather the countrary, we always want to receive the volume for these so the option No-container should not be available (ie the option that hides the volume field)