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

[lmReef]

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

[lmReef]

@nf-core-bot fix linting

[codecov]

Codecov Report

Attention: Patch coverage is 92.10526% with 3 lines in your changes missing coverage. Please review.

Project coverage is 76.27%. Comparing base (ed1667f) to head (aa679d5).
Report is 1 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/pipelines/lint/pipeline_if_empty_null.py	92.00%	2 Missing ⚠️
...ore/subworkflows/lint/subworkflow_if_empty_null.py	88.88%	1 Missing ⚠️

Additional details and impacted files

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[mirpedrol]

LGTM! 🙂

[mirpedrol]

Suggested change

	# Pipelines don"t provide a path, so use the workflow path.
	# Pipelines don't provide a path, so use the workflow path.