Moritz E. Beber
Moritz E. Beber
I have a click argument set up in the following way: ```python @click.argument("model", type=click.Path(exists=True, dir_okay=False), envvar="MODEL", required=False) ``` and I have also configured a corresponding configuration file. This works perfectly....
Done: There is a comprehensive set of benchmarks (using e.g. [pytest-benchmark](https://github.com/ionelmc/pytest-benchmark/) that can be used to decide between C bindings. Binding options in order of feasibility: * SWIG (current) *...
I've created a small proof-of-concept for reading SBML models. I don't expect this to be merged but I hope it can inspire you when the need arises. There is a...
### Description of feature Prompted by the strategy presented in https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1 it would be an interesting general strategy to add a post-profiling step that aligns reads to identified genomes. This...
### Description of feature I don't have a lot of experience with all the tools so I can only speak for kraken2 and Bracken: ### kraken2 * It can be...
In cobrapy we obviously use python-libsbml quite a bit and when running our test suite with pytest we get thousands of deprecation warnings coming from libsbml. For anyone else coming...
### Is there an existing issue for this? - [X] I have searched the existing issues ### Problem description See [discussion on Slack](https://nfcore.slack.com/archives/C031QH57DSS/p1701903800138819) reported by @AmaliT. The following config causes...
In order to use the [OPAL tool](https://github.com/CAMI-challenge/OPAL) for analysis and visualization, it might be useful to convert any supported profiler to [that format](https://github.com/bioboxes/rfc/tree/master/data-format).
I think sourmash is an interesting tool, as it is so fast in scanning vast libraries of genomes. We should add support for its output.