Add nf-test to pipeline template CI workflow

[adamrtalbot]

Will close #2854

Replaces CI workflow with nf-test version.

Changes:

• Uses a Python script to find changed files between PR branch and base.
• Flags any nf-test files present
• Adds 'special' cases such as pipeline level tests
• Identifies any dependencies of changed tests
• Returns as list of nf-test files to run
• Runs nf-test as a matrix over those files
• Confirm pass based on results of previous

PR checklist

• [x] This comment contains a description of changes (with reason)
• [x] CHANGELOG.md is updated
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] Documentation in docs is updated

[adamrtalbot]

@nf-core-bot changelog

[adamrtalbot]

first, we need docs on how to write nf-test for pipelines

And I think this would make more sense with a test added to the pipeline.

[mirpedrol]

We should also add nf-test to the pipieline template, the current template doesn't have them, so this won't work with most of the pipelines which don't have nf-test.

[adamrtalbot]

FYI this is out of date and needs updating with this: https://github.com/adamrtalbot/detect-nf-test-changes and then use nf-test v0.9.0 which includes related features.

[adamrtalbot]

@mirpedrol the unittests are failing on my laptop even on dev so I'm struggling to fix these issues. I get lots of import errors:

AttributeError: module 'nf_core.modules' has no attribute 'modules_utils'

[mirpedrol]

@adamrtalbot tests are fixed now. What are we missing to merge this PR?

[mashehu]

@mirpedrol https://github.com/nf-core/website/pull/2626

[adamrtalbot]

@mirpedrol nf-core/website#2626

That's not true, https://github.com/nf-core/tools/pull/2992 is blocked by that PR. This PR is blocked by #2992.

[mashehu]

I will try to fix the mypy errors