Sentieon Refactor

[maxulysse]

cf https://github.com/nf-core/modules/pull/5856

### Tasks
- [x] ~~Sentieon tests running locally~~
- [x] https://github.com/nf-core/modules/pull/5856
- [x] Sentieon tests running on pipelines (Sarek as an example)
- [ ] Sentieon running on AWS Megatests

Been out for 6-8 months, worked nicely for 6 months. Don't know what's in the GitHub secrets.

### Modules to be updated
- [x] https://github.com/nf-core/modules/pull/5856
- [ ] applyvarcal
- [ ] https://github.com/nf-core/modules/pull/6027
- [ ] dnamodelapply
- [ ] dnascope
- [ ] gvcftyper
- [ ] haplotyper
- [ ] varcal
- [ ] https://github.com/nf-core/modules/pull/5823
- [ ] https://github.com/nf-core/modules/pull/5945
- [ ] https://github.com/nf-core/modules/pull/6025

Checklist for each Module(make a seperate PR for each):

• [ ] Convert to nf-test(pytest-workflow isn't setup)
• [ ] Update the license logic
• [ ] Add @DonFreed as a maintainer in meta.yml

[edmundmiller]

https://github.com/DonFreed/docker-actions-test

Might be of use.

@DonFreed any ideas?

[maxulysse]

testing it out in sarek: https://github.com/nf-core/sarek/pull/1574 in modules: https://github.com/nf-core/modules/pull/5856

[DonFreed]

You can find the example secrets here, https://github.com/DonFreed/docker-actions-test/blob/main/.github/workflows/docker_build.yml#L39-L42. I believe the sarek license server uses the same secrets.

The secrets are:

• The licenser server IP and port
• The message to be encrypted (something like "hello world")
• And the encryption key

[asp8200]

If you guys give me the "credentials", I'll be happy to try and run the Sentieon-tests locally. That might be a bit easier than getting them running on GitHub.

[DonFreed]

What is the status of the instance hosting the license server? If the instance was stopped and restarted, someone will need to restart the instance and update the secret containing the instance IP address.

[maxulysse]

If you guys give me the "credentials", I'll be happy to try and run the Sentieon-tests locally. That might be a bit easier than getting them running on GitHub.

The whole plan is to restart the tests on GitHub @asp8200

[maxulysse]

What is the status of the instance hosting the license server? If the instance was stopped and restarted, someone will need to restart the instance and update the secret containing the instance IP address.

I think that's where we left it at last night.

[edmundmiller]

https://github.com/nf-core/sarek/pull/1746#issuecomment-2528496975

Current status on this:

• Run stubs for Sentieon right now to ensure the channels work correctly.
• Fix the CI later ™️
• For now, use Sentieon at your own risk; we'd love feedback if anything gets broken accidentally; it should work.

For testing, we need to set it with 1Password in the test configs and optimize for Sarek devs running Sentieon tests.

We can duplicate 1Password access in GHA if that's easier than a separate GHA setup and 1Password local development, but I want humans(that have been given access) to be able to run it first and foremost, and second, the robots to be able to run it.