bugfix 2.8.0 - Githubissues

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

http://snakepipes.readthedocs.io

MIT License

374 stars 85 forks source link

bugfix 2.8.0 #978

Closed WardDeb closed 4 months ago

WardDeb commented 5 months ago

multiqc and py 3.7 are not compatible anymore and needs a more recent python version. This is an attempt to (drastically) boost the shared_env versions. Currently still testing all the workflows for any hiccups

[x] ncRNA
[x] ATAC
[x] ChIP
[x] DNA
[x] mRNA
[x] mRNA - allelic
[x] HiC
[x] scRNA
[x] WGBS

WardDeb commented 4 months ago

WGBS workflow had two issues:

PCA errors out when there are 2 samples.
Sambamba include overflow to avoid file limit being hit.

WardDeb commented 4 months ago

HiC workflow encounters one issue related to outdated HiCExplorer version: AttributeError: 'Styler' object has no attribute 'render'. Did you mean: '_render'?

Fixed by boosting HiCExplorer in the environment.

WardDeb commented 4 months ago

All workflows tested, renamed to bugfix 2.8.0 as this is now more relevant.