v0.2.2

Fixed

• Incorrect UMAP colors
• Barcode quality extract error
• Saturation plotting error
• Gene ID assigned instead of gene name
• Empty dataframe bug when no data for a chromosome exists

Changed

• Improved isoform selection criteria

v0.2.1

Changed

• Add multiprocessing to calc_saturation.py for ~ 2X speedup
• Use rapidfuzz for finding barcode matches in whielist; ~10x speedup
• Use multithreading to speed up sequencing saturation calcualtion
• Put UMAPs in report and make optional

v0.2.0

Added

• workflow-glue to allow scripts to be run as a module.
• pytest testing using workflow container.

Fixed

• Incorrectly stranded reads causing stringtie2 to generate incorrect transcripts.

Changed

• Combine barcode and umi extraction into single step.

v0.1.9

Fixed

• Incorrect UMIs reported and not collapsing into unique UMI counts.

v0.1.8

Fixed

• sample_sheet format in schema to expect a file

v0.1.7

Changed

• Updated description in manifest

v0.1.6

Added

• A workflow report using ezcharts.

Chnaged

• Updates for the new Labs Launcher

v0.1.5

Changed

• Replace samlmon for minimap2 for assigning reads to transcripts.

Added

• Reduced matrix to the top N principal components pripor to umap generation.

v0.1.4

Fixed

• Fix transcript matrices not in output folder.

Added

• output of merged bam optional.
• Repeat umap creation with different random states.

Changed

• Transcript counting Salmon on stringtie-generated transcriptome.
• Several perforance-related reforactorings including reductions in read write operations.
• single_cell_sample_sheet is optional and kit options can be supplied as workflow parameters.

v0.1.3

Changed

• Better handling of sample_id conflicts in single_cell_sampkle_sheet and fastgingress.
• single_cell_sample_sheet is optional.
• Minor IO performance enhancements.

Added

• kit options can be supplied from command line/config and applied to all samples.