Release notes

Version 0.9

0.9.3

  • Adds spatial barcode correction with edit distance 1, boosting counts by ~5-15% for many samples. see the documentation for details and caveats.

0.9.2

  • Fixes OverflowError in QC reports

0.9.1b

  • Fixes permissions of html files (QC report and automated analysis)

0.9.1

  • Uses cram instead of bam to significantly reduce disk space.

  • The migrate tool enables updating data processed with v0.8x to be compatible with v0.9.

  • Replaced R scripts with Python for all QC and automated reports.

  • Fixed bugs.

Version 0.8

0.8.1

  • Fixed all automated analyses errors.

  • Fixed a bug that occurred with toy data during the filter_mm_reads step.

0.8.0

  • Faster cmdline interface

  • 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

Version 0.7

0.7.9

  • Fixed issues with STAR shared memory indexes

0.7.7

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.

0.7.6

  • Fixed a critical bug when processing merging samples

  • Updated documentation to describe the Open-ST workflow

0.7.5

  • Fixed several bugs.

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

0.7.2

  • Updated the environment.yaml to pin the pandas version.

  • Fixed bugs and errors.

0.7.0

  • 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.

Version 0.5

0.5.5

  • Fixed issue with --version introduced in v0.5.4

  • Fixed command line error where updating a sample would remove puck_ids

0.5.4

  • Each sample can have multiple barcode files

  • Added a novosparc tutorial

  • Fixed bug on read-only project_df.csv` during spacemake run

  • Fixed bug in adding new puck command

0.5.3

  • Further bug fixes

  • Completed docs with longread tutorial

0.5.2

  • Fixed errors during initialization and species download

  • Updated docs

0.5.1

  • Added H&E integration

  • Updated documentation

  • Bug fixes

Version 0.4

0.4.3

  • Bug fixes

0.4.2

  • Added novosparc command line tools

  • Bug fixes

0.4.1

Initial release of spacemake containing

  • base spacemake for processing sequencing based spatial transcriptomics data

  • default values for methods such as: Visium, Slide-seq, Seq-scope and general scRNA-seq

  • modules: technical replicate merging, downsampling, long-read analysis