Replace DeliverAPI with DeliveryAPI

[ivadym]

As a bioinformatician, I want a maintainable and unambiguous delivery API, So that the delivery to Caesar is more understandable and error-free.

Some work has already been done: https://github.com/Clinical-Genomics/cg/blob/ff34ed99c425f0fd0380b3db663791b38d28ebf0/cg/meta/delivery/delivery.py#L22

Acceptance Criteria

• [ ] Files delivered successfully to Caesar
• [ ] Removed unnecessary logic from certain deliveries (FastQ, Fastq-QC, etc.)

Notes

• Related user stories. Some should be addressed, ideally, taking into account the new delivery API:
  • https://github.com/Clinical-Genomics/cg/issues/3432
  • https://github.com/Clinical-Genomics/cg/issues/2603
  • https://github.com/Clinical-Genomics/cg/issues/3339
  • https://github.com/Clinical-Genomics/cg/issues/2304

Implementation plan

• [x] Extract the files to be delivered per workflow and delivery type: https://github.com/Clinical-Genomics/cg/pull/3029
• [x] Report the delivered files in the delivery report: https://github.com/Clinical-Genomics/cg/pull/3029
• [ ] Add commands for the updated delivery API
• [ ] Implement Rsync to Caesar following new file centered delivery logic
• [ ] Replace the DeliverAPI with the DeliveryAPI in the clinical uploads

[ChrOertlin]

closing in favour of: https://github.com/Clinical-Genomics/cg/issues/3627