Add pytest workflow for CI

[maxulysse]

Following @emiller88 lead on improving CI

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).

[maxulysse]

@emiller88 I see what you meant by this where the real magic starts...
🤯

[FriederikeHanssen]

Wow, this is awesome 🤩 ❤️ . The linting i not passing yet:

[✗] 21 Tests Failed                                                          │
├──────────────────────────────────────────────────────────────────────────────┤
│ files_exist: File not found: lib/nfcore_external_java_deps.jar               │
│ files_exist: File not found: lib/NfcoreSchema.groovy                         │
│ nextflow_config: Config variable not found: params.show_hidden_params        │
│ nextflow_config: Config variable not found: params.schema_ignore_params      │
│ nextflow_config: Config variable (incorrectly) found: params.name            │
│ files_unchanged: CODE_OF_CONDUCT.md does not match the template              │
│ files_unchanged: .github/.dockstore.yml does not match the template          │
│ files_unchanged: .github/CONTRIBUTING.md does not match the template         │
│ files_unchanged: .github/ISSUE_TEMPLATE/bug_report.md does not match the te… │
│ files_unchanged: .github/ISSUE_TEMPLATE/feature_request.md does not match t… │
│ files_unchanged: .github/markdownlint.yml does not match the template        │
│ files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the templa… │
│ files_unchanged: .github/workflows/branch.yml does not match the template    │
│ files_unchanged: .github/workflows/linting.yml does not match the template   │
│ files_unchanged: assets/nf-core-sarek_logo.png does not match the template   │
│ files_unchanged: bin/markdown_to_html.py does not match the template         │
│ files_unchanged: docs/images/nf-core-sarek_logo.png does not match the temp… │
│ files_unchanged: .gitignore does not match the template                      │
│ files_unchanged: assets/multiqc_config.yaml does not match the template      │
│ actions_ci: '.github/workflows/ci.yml' is not triggered on expected events   │
│ actions_ci: Minimum NF version in '.github/workflows/ci.yml' different to p… │

Did you expect that?

And one other idea: maybe add a short readme on how to add new tests for new developers, or is it the exact same as with the modules-repo?

[maxulysse]

Yeah, nf-core lint would be another PR.
Same as for modules. but yeah a README somewhere might be nice

[FriederikeHanssen]

OK great. Then maybe let's add a README in a seperate PR, like a short Step-by-step or so.

[maxulysse]

OK great. Then maybe let's add a README in a seperate PR, like a short Step-by-step or so.

I'm guessing a step by step should even go in another repo.
It's not sarek specific