Serialize Snakefiles from YAMLs

[imallona]

Developing at branch dev https://github.com/omnibenchmark/omni_workflow/tree/dev

[imallona]

Consensus (whole team): use starts_to_be_explicit YAML

[imallona]

PR prototype

[DanInci]

What the Serialization of Snakemake file includes

Mandatory:

• [x] Include LinkML Omni-Schema
• [x] Dynamically generate rules
• [x] Link inputs to outputs
• [x] Nest multiple method runs, due to multiple input values
• [x] Manage exclusions
• [x] Hash params and runs

Nice to have:

• [x] Allow paths to be colapsed if multiple parameters / runs do not exist for module
• [ ] Write multiple benchmark examples to verify integrity of the generated Snakefile
• [ ] Logic validation for benchmark.yaml file
• [ ] Cofigurable / Customizable output paths for files
• [ ] Found corner cases:
  • If inputs are taken from previous steps, then the execution is redundant (e.g. both M1 and M2 when taking the inputs from data stage and skipping processing step, then execution paths become redundant)