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For scATAC, support fastq, bam, fragments.tsv.gz as the input of the scATAC-seq workflow;
For scATAC, provide an option for users to skip the cell-type annotation step in the pipeline, and an option to choose the strategy for cell-type annotation (ATACAnnotateCelltype and ATACAnnotateChromatinAccessibility);
Provide small test data for test scRNA-seq and scATAC-seq pipeline (sampling from 10x fastq files);
Add parameter validation before initializing the pipeline and provide more gracious error messages;
Update R in MAESTRO conda package to 4.0.2, and Seurat to 3.1.5