added patch command for subworkflows

[ctuni]

Related to issue: https://github.com/nf-core/tools/issues/1891

Is there a straightforward way to test this?

[github-actions[bot]]

This PR is against the master branch :x:

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

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Hi @ctuni,

It looks like this pull-request is has been made against the ctuni/tools master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the ctuni/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 77.67857% with 25 lines in your changes missing coverage. Please review.

Project coverage is 75.62%. Comparing base (207129d) to head (8b2bec4). Report is 31 commits behind head on dev.

Files with missing lines	Patch %	Lines
nf_core/subworkflows/lint/subworkflow_changes.py	33.33%	10 Missing :warning:
nf_core/__main__.py	43.75%	9 Missing :warning:
nf_core/modules/lint/module_patch.py	50.00%	4 Missing :warning:
nf_core/modules/modules_json.py	88.23%	2 Missing :warning:

Additional details and impacted files

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

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[mashehu]

for testing you can do similar things to https://github.com/nf-core/tools/blob/master/tests/modules/patch.py

[mirpedrol]

Hello! @ctuni are you planning to work on this PR, otherwise I would like to take over and finish it up :)

[ctuni]

Hello! Thank you for reviving this, please go ahead and let me know if I can help with anything!

[ewels]

@ctuni this might help your future development work 😉

pip install pre-commit
pre-commit install

It'll run ruff and other tests as part of git commit and fix formatting errors before you push..