Ken Brewer

I've encountered this bug too with the docker alias suggestion. I think it's related to Issue #734 . Also fixed by removing the `-u` parameter from my docker alias.

There's a nf-core linting failure that needs to be addressed before review: > [nextflow_config](https://nf-co.re/tools/docs/2.13.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: params.aligner is set as bwa-mem in nextflow_schema.json but is null in...

@asp8200 Could the problem maybe be happening when we try to [assign a tag](https://github.com/maxulysse/nf-core_sarek/blob/4575cbab5415212f62e2e929343b04b3859f2d58/modules/local/create_intervals_bed/main.nf#L2) to the job? Maybe AWS batch only supports tags of a certain length, or the files...

@maxulysse What still remains to be done on this PR? This is a pretty substantial bit of refactoring, and I think it would be good to get this merged back...

This is a super cool idea! Excited for this one!

@fpgmaas I think a good part of this issue was addressed in 0.12.0. Have the in-file ```import tomllib # deptry: ignore[DEP001]``` style ignores already been added as well or is...

Hi Paula, Could you let us know what version of pandas you have installed in your virtual environment? This is a future facing change we made to prepare for pandas...

I approved @d33bs fix and we'll get that merged as soon as possible. I agree with his assessment that something about your setup means that the dependency versions you reported...

@d33bs @gwaybio I'm a bit swamped a the moment preparing for the Nextflow summit next week. So probably not a good idea to wait on me for this patch. I'll...

@d33bs I was working on #391 and put together a makefile command for the docs build. I got the following error message: ``` 📚 Building documentation Running Sphinx v7.1.2 building...