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We use some... unconventional... syntax in several rules. This may not even be worth your attention, but FYI. minimal example: ```python rule break_snakefmt_044: shell: ("conditional prefix" if True else "")...
Indexing all 100+ versions would be super slow, heavy and prone to errors due to connection stability. Alternatively, we could only index it for genomes ending with `.p*` (e.g. GRCh38.p12)....
Bakers yeast is one of those model organisms you would expect to be used a lot. Unfortunately, the filing system for this genome, and at least several other fungi is...
pip pyproject.toml and setuptools dont work nicely together [yet](https://stackoverflow.com/questions/71517365/pyproject-toml-wont-find-project-name-with-setuptools-python-m-build-format). I tried to make it work, but `entry points` and `packages` aren't implemented/documented properly yet. Here's what I got so far....
```python import genomepy def mito_genes(annotation_path): ann = genomepy.annotation(annotation_path) gtf = ann.named_gtf # very quick, very dirty way to find the name for the mitochondrion. # could also try to read...
**what** Would we like to implement a pre-commit hook/test step which performs formatting? **how** Snakemake's own version of `black`, `snakefmt`, is working in most cases. By running it on 1...
**Describe the bug** Jenkins sometimes gets stuck on rule softmask_track_1 [rule](https://github.com/vanheeringen-lab/seq2science/blob/5c13d49417ccd76cde90aace2279effdf4928726/seq2science/rules/trackhub.smk#L128). http://ocimum.science.ru.nl/jenkins/blue/organizations/jenkins/seq2science/detail/PR-884/1/pipeline/ http://ocimum.science.ru.nl/jenkins/blue/organizations/jenkins/seq2science/detail/develop/250/pipeline/ http://ocimum.science.ru.nl/jenkins/blue/organizations/jenkins/seq2science/detail/develop/148/pipeline/97 **possible solutions?** - end the rule with `pool.join()` - add a timeout + retry - switch...
There should be an input requirement for that the assembly is from ensembl. An input function should be able to do this right? _Originally posted by @Maarten-vd-Sande in https://github.com/vanheeringen-lab/seq2science/pull/835#discussion_r837283713_ This...
I dont think we're still using the tool, but if we are, we could implement it into the pyproject.toml with [this wrapper](https://dev.to/bowmanjd/using-flake8-and-pyproject-toml-with-flakehell-1cn1).
Only thing worth discussing here is whether it makes sense the cluster ID is in the samples.tsv or if that should be a separate file. Idk what's easier from the...