Add a subworkflow to upload raw reads to ENA

[mberacochea]

Description of feature

The plan is to support raw reads to INSC (ENA to start with).

ENA data model

The pipeline will have to handle the registration of several pieces of data, plus the validation of the metadata. ENA provides programmatic upload endpoints and tools - https://ena-docs.readthedocs.io/en/latest/submit/reads/programmatic.html. These would need to be wrapper in nextflow modules as the starting point.

I will keep adding details to this ticket over the coming days.

[ochkalova]

I suggest using webin-cli and approach with manifest files described here https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html

It's easier to implement and debug and it's also the same way we upload assemblies and bins/mags

[ochkalova]

From what I learned, the workflow should have 4 modules:

1. decontamination
2. study creation (if --submission_study is not provided)
3. manifest creation
4. submission with WEBIN cli module (already exists)

I think the most suitable person for this task is @timrozday-mgnify
I would shape this task as:

1. create study creation module and nf-test (test can be reused from the current module) - Tim already has a similar script that can be used as a basis; there is a separate task for it
2. create manifest creation module and nf-test
3. write the RUNSUBMIT workflow, samplesheet schema, workflow test and update the README

I omitted decontamination for now, it can be included as well.