Add multiple pipeline modes

What's Changed

• Implement multiple pipeline modes by @nictru in #56

Full Changelog: v0.2.1...v0.3.0

Budva version

What's Changed

• Fix problems with small batches during doublet detection by @nictru in #52
• Support pseudo aligners by @nictru in #53
• Implement a second iteration to the pipeline by @nictru in #55

Full Changelog: v0.2.0...v0.2.1

Add first features for Budva Conference

What's Changed

• Make celltypes optional by @nictru in #44
• Fix problems with dots in gene symbols by @nictru in #45
• Switch to constant threshold for minimum cells to keep genes by @nictru in #46
• Make HVG identification more robust when low expression values are present by @nictru in #47
• Fix bug with SOLO if batch size is smaller than 128 by @nictru in #48
• Fix problems with tmp mount in apptainer (Diana's Leistung) by @nictru in #49
• Implement support for adding custom metadata columns and including certain genes to HVGs by @nictru in #50
• Implement detection for problems in input files by @nictru in #51

Full Changelog: v0.1.3...v0.2.0

February 2024 STSM release

v0.1.3

Fix poblems with cell types which are exclusively in extended datasets

Fix SOLO problems

Full Changelog: v0.1.1...v0.1.2

Implement proper doublet removal

What's Changed

• Improve doublet removal by @nictru in #31

Full Changelog: v0.1.0...v0.1.1

Version for february STSMs

Contains vast performance optimizations

First version of the pipeline

This is the state that was reached during the STSM in Freising