David Laehnemann

Results 125 comments of David Laehnemann

TypeError in calling.smk rule merge_variants. The bwa mapping stops after creating the indexes files.

Ah, sorry, PR #40 was never quite finished. I'll try and follow it up to get this fixed. Once this PR is merged, I can release a new version of...

feat!: Sequence ontology support

> I'm also not too happy about this. However: > > * sequence ontology is quite stable, i.e. is not expected to fluctuate much > > * the sequence ontology...

Update deseq2.yaml

See: https://github.com/snakemake-workflows/rna-seq-star-deseq2/pull/90#issuecomment-3252995395

update snakemake workflow template with latest Actions + new features

If you would be willing to work on this, that would be great. Also feel free to simply start a pull request with some of your ideas and gradually add...

feat: create nanosim wrapper for all three modes of simulator.py

I think I would prefer actually listing the required files with `multiext()` like this, to explicitly specify which files are needed for which type of simulation (they slightly differ...). In...

feat: create nanosim wrapper for all three modes of simulator.py

@fgvieira any more time for a review, or should I ask around?

feat: create nanosim wrapper for all three modes of simulator.py

Thanks for looking into this further. A thorough review is always appreciated. And any ideas for making this more useful are welcome. We do need those pre-trained models, if we...

feat: create nanosim wrapper for all three modes of simulator.py

I cross-referenced this once more over in the NanoSim repo, and will merge it as is, for now. They have recently provided a newly trained model for genomic DNA, but...

Failure to extend header parameters from tables/output/annotation_fields for 'vembrane table --header "{params.config[header]}" "{params.config[expr]}'

Thanks for digging into this and for taking the time to report this thoroughly! We recently changed how this works, and it seems we haven't gotten to a clean solution,yet....

Failure to extend header parameters from tables/output/annotation_fields for 'vembrane table --header "{params.config[header]}" "{params.config[expr]}'

A couple of thoughts of how you might get most of this done within the existing workflow: 1. I think you could do all of your filtering before the `vembrane...