Refactor Variant Calling

[FriederikeHanssen]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[FriederikeHanssen]

@maxulysse almost happy with the state of this, just need to add haplotypecaller and mutect back in. I think i am going for smaller PRs now, makes both of our lifes a lot easier I think.

[maxulysse]

<3

[FriederikeHanssen]

ok, Haplotypecaller will be fixed in the next PR, after the discussion on slack it will be a little bit more then just refactoring. But it seems straight forward in the next one now.

For Deepvariant: The gvcf are generated no matter what, I don't see why we shouldn't publish them, so i removed it for now.

I don't know whats going on with all the CI tst, locally it's fine:

❯ NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=docker pytest --tag default --symlink --keep-workflow-wd
============================================================================================================================ test session starts ============================================================================================================================
platform darwin -- Python 3.9.10, pytest-7.1.1, pluggy-1.0.0
rootdir: /Users/monarchy/Projects/Coding/sarek
plugins: workflow-1.6.0
collecting ... 
collected 17 items                                                                                                                                                                                                                                                          

Run default pipeline:
        command:   nextflow run main.nf -profile test,docker
        directory: /Users/monarchy/pytest_workflow_tewepav2/Run_default_pipeline
        stdout:    /Users/monarchy/pytest_workflow_tewepav2/Run_default_pipeline/log.out
        stderr:    /Users/monarchy/pytest_workflow_tewepav2/Run_default_pipeline/log.err
'Run default pipeline' done.

tests/test_default.yml .................                                                                                                                                                                                                                              [100%] Keeping temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.

Edit: Set ressource requests to high in test.config to speed up local computation 🤦‍♀️

[maxulysse]

tests/test_default.yml .................

did you empty your results folder before doing the tests?

[FriederikeHanssen]

See edit: increased resources locally to speed up tests and accidentally pushed them. They ran now after reducing them again

[maxulysse]

<3