nf-core bump-version breaks linting

[d4straub]

Description of the bug

nf-core bump-version removes the last newline in nextflow.config and therefore breaks linting, I had to correct that for ampliseq and bacass after bumping the version.

Steps to reproduce

Steps to reproduce the behaviour:

nf-core bump-version
results: nf-core linting on github EditorConfig will fail with

$ editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
nextflow.config:
	Wrong line endings or new final newline
1 errors found

Version

nf-core/tools version 2.1

[ewels]

I don't really understand how this can happen 🤔 We do a regex find + replace for a specific string (that is not at the end of the file). Is Python really messing with the newlines just from opening and resaving a file?

[ewels]

Tested and replicated the error. It's my fault, it's because the code splits the file into an array of lines and then joins them with a newline. This means that the trailing newline is removed.

Fixed in #1438