Fix linting with rocrate_readme_sync throws error if there is any changed file in directory

[jonasscheid]

Description of the bug

I do have a clean commit history, nothing is staged, but if I run

nf-core pipelines lint --fix rocrate_readme_sync

                                      ,--./,-.
      ___     __   __   __   ___     /,-._.--~\ 
|\ | |__  __ /  ` /  \ |__) |__         }  {
| \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                      `._,._,'

nf-core/tools version 3.3.2 - https://nf-co.re

INFO Testing pipeline: .
INFO Attempting to automatically fix failing tests
CRITICAL Critical error: Uncommitted changes found in pipeline directory!
Please commit these before running with '--fix'
INFO Stopping tests...

Command run on branch https://github.com/jonasscheid/mhcquant/tree/template-merge-332 branch

Command used and terminal output

nf-core pipelines lint --fix rocrate_readme_sync

System information

• Nextflow version 25.04.6 build 5954
• Gitpod

[ningyuxin1999]

From Slack: The lint expects no changes in the working directory even tho it's not related to fix linting.

git status
On branch template-merge-332
Your branch is up to date with 'origin/template-merge-332'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   .vscode/settings.json

no changes added to commit (use "git add" and/or "git commit -a")

[mirpedrol]

is this resolved? can I close the issue?

[jonasscheid]

Cannot check until September. @ningyuxin1999 Can you? :)

[ningyuxin1999]

Sorry for not looking into this for so long😅😅 This should be fixed now since the rocrate and readme are automatically synced :#3688

[jonasscheid]

Juhuu