use dorny/paths-filter with git commands instead of GitHub API

[mirpedrol]

From the docs:

# Personal access token used to fetch a list of changed files
# from GitHub REST API.
# It's only used if action is triggered by a pull request event.
# GitHub token from workflow context is used as default value.
# If an empty string is provided, the action falls back to detect
# changes using git commands.

[edmundmiller]

@adamrtalbot any idea why this is failing? I'm stumped.

What's the point of the check for the checks just for the debug print?

[adamrtalbot]

On my phone but do you mean the confirm-pass? It's the only way of enforcing branch protection I can find at the moment. You can't force checks for variable name tests.

[mirpedrol]

It is detecting too many changed files, no? Testing dumpsoftwareversions, fastqc, snakemake and samtools

[mashehu]

It is detecting too many changed files, no? Testing dumpsoftwareversions, fastqc, snakemake and samtools

Yes, but somehow only from nf-test, so something not perfectly clean with the setup there.

[adamrtalbot]

It has detected every file has been added, but the pytest check changes cant create an output object because there are too many (>256), so it fails the test because they did not work.

The check-changes doesn't work correctly yet, it detects all files are new and have been added.

[adamrtalbot]

Pytest changes:

[mirpedrol]

After some research, I found that there is a small problem when using git commands to retrieve changed files. There's a PR opened with the fix already. Same user created a fork of paths-filter with the fix.
This is now detecting only files changed in this PR, but it includes the modules coming from merging branch master to the current branch.
Do you think it's a good option to use this fork until the original GHA is fixed?

[mashehu]

Yes, the changes in the PR look reasonable. Let's go for it