bump ALL gatk4 modules

[matthdsm]

• Bump GATK to v 4.6.1.0
• Fix environment files
• Add renovate comments
• Move to wave containers
• Add missing nf-tests
• Fix broken tests
• drop legacy test_data path
• ...

PR checklist

Closes #XXX

• 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 - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[maxulysse]

Looking good, but failing tests 😭

[edmundmiller]

This works:

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
  - bioconda
dependencies:
  # renovate: datasource=conda depName=bioconda/gatk4
  - bioconda::gatk4=4.5.0.0

4.6.1.0 doesn't 🫠

[matthdsm]

Nice find with the hidden character @edmundmiller! I've managed to fix it for all the tests.

[nvnieuwk]

Some comments :p