seq2science
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vanheeringen-lab
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
**What problem is the PR solving / What's new?** A description of the problem that is being solved, or which new feature is implemented. Please link to other relevant issues/pr...
**Question** Seq2science installs a couple GBs of conda envs after a run. Should we uninstall those by default on a succesful run? Could be a flag that can be turned...
Looks good! Based on the number of files it got a bit cleaner too :D I googled for SCTK and MultiQC, and noticed that the SCTK authors refer to MultiQC...
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....
**Is your feature request related to a problem? Please describe.** Might be a more sustainable way of doing these things I guess in a sense related to #537, and should...
```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...
When i run scrnaseq with preprocessing enabled on a velo workflow: ``` quantifier: kallistobus: ## Velocity example ## ref: '--workflow lamanno' count: '-x 1,8,16:1,0,8:0,0,0 --verbose --workflow lamanno --loom' sc_preprocess: export_sce_objects:...
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...
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Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.