Add linting for ifEmpty(null)

[lmReef]

Add pipeline and subworkflow linting for ifEmpty(null)

Resolves issue #2506

Description from original issue

There are two general cases for workflows to use the channel operator ifEmpty. The first is ifEmpty( [ ] ) to ensure a process executes, for example when an input file is optional (although this can be replaced by toList()). The second is when a channel should not be empty and throws an error ifEmpty { error ... }, e.g. reading from an empty samplesheet.

There are multiple examples of workflows that inject null objects into channels using ifEmpty (see https://github.com/search?q=org%3Anf-core+ifEmpty&type=code&p=2), which could cause unhandled null pointer exceptions as was the case in #1966.
The feature request is that linting throws up a warning when this operation is found.

Warning message example:

Implementation based on pipeline_todos as it's very similar (link to main file)

Uses regex pattern ifEmpty\(\s*null\s*\)

PR checklist

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

[mashehu]

@nf-core-bot fix linting

[mirpedrol]

Hi @lmReef, thanks for contributing!
It is looking good, but we should also add a test for this. You can find samples for other linting tests in tests/pipelines/lint, I think https://github.com/nf-core/tools/blob/main/tests/pipelines/lint/test_template_strings.py will be useful for this case

[mirpedrol]

We are not ignoring paths on .gitignore for other linting tests, I think it's a good idea, but I am wondering if we should add it to all tests for consistency.

[mirpedrol]

I see we have an issue for that #3385 let's leave it for a separate PR

[lmReef]

sounds good, I'll remove it from here and maybe have a look at a more general implementation in a different pr

[mirpedrol]

I don't think we have latin1 enconding

Suggested change

	with open(Path(root, fname), encoding="latin1") as fh:
	with open(Path(root, fname)) as fh:

[lmReef]

interestingly without either encoding="latin1" or errors="ignore" it fails to decode files both during the pytest and when testing the linting on a new pipeline.
I took this from the file pipelines/lint/pipeline_todos.py. Is this a me issue or should I add latin1 back in?

[lmReef]

actually I just realized template_strings.py uses encoding="latin1" for reading files too, I'll add it back in for now

[mirpedrol]

my bad, let's add encoding="latin1" back, thanks!

[lmReef]

awesome thanks for the feedback, I'll make those changes