fix: gtf sorting

[mkatsanto]

Description

The provided gtf annotation files provided by Ensembl can cause errors by ALFA.
To avoid this issue, we introduce an extra rule that sorts the gtf file by chromosome, start and end.

Fixes #113

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• Documentation updated

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  https://www.conventionalcommits.org/en/v1.0.0/

Changes to workflow inputs (sample table and/or configs)

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • more fields/properties are required
  • existing ones are dropped entirely
• minor (add feat: in the beginning of the PR title)
  • optional fields/properties are added
  • required ones are made optional

Changes to workflow outputs

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • changes lead to removal/change of existing outputs (format or location)
• minor (add feat: in the beginning of the PR title)
  • additional outputs are generated
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Everything else: patch
(add any other conventional commit in the beginning of the PR title)

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
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• New and existing tests pass locally with my changes
• I have updated the project's documentation

[dominikburri]

Hi @mkatsanto, Thanks for the PR!
I ran the local-conda test successfully (exit code 0) and manually checking the results looked fine.
I only have minor comments on the pipeline documentation.

[dominikburri]

Thanks for the fixes!