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New features
CITE-seq and Cytometry:
- CITE-seq and Cytometry pipelines have been added to the software. Counts and other outputs are generated but there is no HTML report at this time.
Enhancements to existing features:
- Mixed Species YAML Format
When supplying YAMLs for mixed-species experiments, the two sets of references (FASTA and GTF files) are now specified on a single line, separated by a space.
See the example-parameters directory for updated formatting examples. - Updated Output Directory Structure
With multi-omics support, the sample_files directory now includes an additional folder layer under each sample ID, organized by modality (e.g., RNA, Cytometry, ATAC).
Beta bug fixes:
Fixed an issue with container names not evaluating correctly