Tom Kelly

Thanks for clarifying. I was wondering if templates would change making it problematic to use older ones. I'll try resolving the linting syntax errors and testing it. If the finishing...

Thanks for the explanation @JoseEspinosa, I'll update tests on the current version first and then pull updates and merge the next version from nf-core. As you can see above I've...

I confirmed that the Cell Ranger test can pass without errors running locally on the Docker node. I'll need more time to set up the UniverSC test runs but it...

@JoseEspinosa Thank you for your advice. I suspect this is what is causing issues with automated checks. I'll try merging the restructured master branch and moving files for the new...

As expected Linting seems to pass checks again. However, "check changes" on GitHub actions seems to have trouble detecting which modules to run tests on in the new restructured repository.

Sorry for the confusion. I was able to fix this issue here: https://github.com/nf-core/modules/pull/1706/commits/a79e689429ec6aa262a75028272c1f15a5113b08 Tests now start correctly. I am debugging why they fail currently.

I think automated tests passing is the only remaining step to complete this PR. I'll update the input arguments for UniverSC as needed to troubleshoot tests. The inputs are very...

Tests for CELLRANGER_COUNT_OS pass locally. I checked the contain supports an open-source implementation of `cellranger mkref`. ``` $ nextflow run tests/modules/nf-core/universc -entry test_cellranger_10x -c tests/config/nextflow.config N E X T F...

Cell Ranger "auto" chemistry detection fails on small input files so I have altered the test jobs for when technology="10x". Other technologies configure chemistry settings automatically. This requires write permissions...

Since only minor issues with testing remains I will open this PR for review. Your feedback is appreciated.