enable setting defaulBranch for pipeline repo creation

[fabianegli]

For reference: https://nfcore.slack.com/archives/CE5LG7WMB/p1665850093986309

When a local .gitconfig specified the init.defaultBranch to anything else than master one sync test would fail.

To make the tests system config agnostic, it is necessary to have a different way of telling nf-core tools what it should use as a default branch when creating new pipeline repositories. This PR implements just that in the internals and uses the feature to make tests pass on systems with init.defaultBranch not set to master. It does not expose this feature to the CLI - this should maybe be the topic of another PR that then also updates the docs.

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

[codecov]

Codecov Report

Merging #1959 (b4789a6) into dev (6cd9134) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #1959   +/-   ##
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  Coverage   61.10%   61.10%           
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  Files          37       37           
  Lines        4677     4677           
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  Hits         2858     2858           
  Misses       1819     1819           

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[fabianegli]

I wonder why the pipeline creation CI fails 🤷

[Aratz]

Great work! Suggested a couple of changes.

Additionally, I think it would be great if you could edit test_create.py to check the default branch is set correctly

tools/tests/test_create.py

Lines 31 to 35 in dec66ab

	def test_pipeline_creation(self):
	assert self.pipeline.template_params["name"] == self.pipeline_name
	assert self.pipeline.template_params["description"] == self.pipeline_description
	assert self.pipeline.template_params["author"] == self.pipeline_author
	assert self.pipeline.template_params["version"] == self.pipeline_version

[fabianegli]

Ready for re-review.

[Aratz]

Looks great! You did not address adapting the tests in test_create.py though

[fabianegli]

Thank you for the flowers.

Forgot the note about the test. Added one.

[fabianegli]

There's maybe still an issue with the default branch not being included in the template. I am not familiar enough with the templates and would like some input from someone who is about wether the default branch should be part of the template or not.