v0.8

• Faster cmdline interface
• 10x improvement in speed for fastq_to_BAM
• Added mrfifo implementation for the preprocessing steps
• Lower memory footprint for BamTagHistogram and for n_intersect_sequences
• Added several unit tests with pytest
• Added kebab-case functionality
• Fixed bugs

v0.7.9

• Fixed issues with STAR shared memory indexes

v0.7.7

This release provides better RAM usage and faster processing through the following features:

• Lower RAM consumption during the fastq to BAM step.
• Lower RAM consumption and increased ~5x faster processing during the h5ad creation step.
• STAR now loads the genome index only once in memory and shares it across workers.

v0.7.6

• Fixed a critical bug when processing merging samples
• Updated documentation to describe the Open-ST workflow

v0.7.5

• Fixed several bugs.
• Added support for open-ST run_mode, and barcode_flavor.

v0.7.2

• Updated the environment.yaml to pin the pandas version.
• Fixed bugs and errors.

v0.7

• Added support for multiple references per species (genome, rRNA, mirgenedb etc).
• The multiple species references are controlled through the map_strategy variable (e.g. rRNA->genome).
• Implemented an optimized algorithm for binning (meshing) coordinate systems.
• Added support for easy addition of custom rules into the workflow.
• Added unit tests.
• Updated the environment.yaml to pin the OpenJDK version.
• Fixed several bugs and errors.

v0.5.5

• fixed issue with --version introduced in v0.5.4
• fixed command line error where updating a sample from the command line would remove puck_ids

v0.5.4

• Each sample can have multiple barcode files
• Added a novosparc tutorial
• Bugfixes:
  • read-only project_df.csv during spacemake run
  • adding new puck command

v0.5.3

• Further bugfixes
• Completed docs with longread tutorial