[Pipeline integration] Starting pipelines

[Vince-janv]

Description

The process of starting pipelines is currently extremely flexible. Most of them consist of the the same CLI commands and the same methods to support them, but this results in a lot of code duplication. This flexibility also allows each pipeline to implement the methods slightly differently causing maintainability issues.

Given this we can also define rules that pipelines need to abide to, to be able to be implemented.
For examples:

• The input parameters should be able to be parsed from a file
• Sample information can be submitted in a samplesheet

Additionally we only rely on cg invoking the CLI of the pipeline. For Nextflow analyses we can send requests to seqera-platform instead.

Acceptance criteria

• Create an interface where the only methods one needs to implement is:
  • configure_case
  • start_analysis
• New NextFlow pipelines should use the seqera-platform API instead of invoking the CLI