Jeffrey Hsu

write_source_archive issue on windows when using a remote executor

1

**Snakemake version** 8.4.7 **Describe the bug** On Windows write_source_archive in workflow.py tries to write to C://Tempfile//Path/snakemake-sources.tar.xz rather than C:/Tempfile/Path/snakemake-sources.tar.xz **Logs** **Minimal example** **Additional context** I believe the following line in...

bwa aligned bams aren't properly filtered because of this and just sym-linked

fix: deeptools bamcoverage fix

1

Fixes a small issue when including the genome and read_length pulling from the pre-computed effective genome sizes. The returned genome size is an int rather than a string. ### QC...

Would be useful if this was integrated into https://github.com/theislab/scanpy. One thing that would need to be done is a python version of MetaNeighbor.

[BUG] continuous_factor errors out in _build_contrast

2

**Describe the bug** Setting continuous_factors in a DeseqDataSet exclusively causes an error in DeseqStats when building a contrast. However, if the same factor is included in the design_factors, it is...