Add VCF QC

[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 I was thinking like so

[FriederikeHanssen]

@maxulysse there is a problem with intervals files that showed up in the MQC report. I started working on it a tiny bit but realised that it should better go in a separate PR

[FriederikeHanssen]

Results of running nf-core lint locally:

INFO     Testing pipeline: .                                                                                        __init__.py:243
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ General lint results                                                                                                            │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [?] 4 Tests Ignored                                                                                                             │
├─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ files_unchanged: File ignored due to lint config: assets/nf-core-sarek_logo_light.png                                           │
│ files_unchanged: File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png                                      │
│ files_unchanged: File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png                                       │
│ files_unchanged: File ignored due to lint config: lib/NfcoreTemplate.groovy                                                     │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 7 Test Warnings                                                                                                             │
├─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required                           │
│ pipeline_todos: TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or direct… │
│ pipeline_todos: TODO string in test_full.config: Give any required params for the test so that command line flags are not need… │
│ pipeline_todos: TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or direct… │
│ pipeline_todos: TODO string in test_full.config: Give any required params for the test so that command line flags are not need… │
│ schema_description: No description provided in schema for parameter: umi_read_structure                                         │
│ schema_description: No description provided in schema for parameter: group_by_umi_strategy                                      │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [✗] 3 Tests Failed                                                                                                              │
├─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤
│ files_unchanged: .github/workflows/branch.yml does not match the template                                                       │
│ files_unchanged: .github/workflows/linting_comment.yml does not match the template                                              │
│ files_unchanged: .github/workflows/linting.yml does not match the template                                                      │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Module lint results                                                                                                             │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Failed                                                                                                               │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────┬───────────────────────────────────────┬──────────────────────────────────────────────╮
│ Module name                              │ File path                             │ Test message                                 │
├──────────────────────────────────────────┼───────────────────────────────────────┼──────────────────────────────────────────────┤
│ ascat                                    │ modules/nf-core/modules/ascat/main.nf │ Local copy of module does not match remote   │
╰──────────────────────────────────────────┴───────────────────────────────────────┴──────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 431 Tests Passed  │
│ [?]   4 Tests Ignored │
│ [!]   7 Test Warnings │
│ [✗]   4 Tests Failed  │
╰───────────────────────╯

Tip: Some of these linting errors can automatically be resolved with the following command:

    nf-core lint  --fix files_unchanged
    ```
    

[maxulysse]

Wonderful