Snakemake Pipeline
- All the different components of ABC were moved into Snakemake, allowing easy execution of the entire ABC codebase with 1 snakemake command
Customization of ABC via config files
- Customization of ABC done in config files, instead of CLI arguments
Streaming of .hic files
- Support reading .hic files directly for the contact portion of the model
Support ATAC and scATAC as input
Support passing multiple input files (e.g 2 DHS BAM files)
Documentation overhaul to ReadTheDocs
QC Plots for all ABC runs
Updated hg38 reference files
Conda Environments
- Conda environment yml file that can get built successfully on linux and macosx
- To prevent environment breakages, the conda environment gets built everyday via CircleCI
End to End Tests
- Tests that run ABC end to end and verifies there are no correctness regressions
Fixes to powerlaw computation, NaN ABC scores, sex chromosome normalization, and more