v0.1.1

• Fixed the problem where one vs. rest plots fail if negative exists.
• Other minor updates.

v0.1.0

• Adds automated basic QC notebook for Cell Hashing (aka. hashtag) and CITE-SEQ.
• Disables read_from_cache, enables write_to_cache by default.

v0.0.13

• Added missing submit-cellplex.sh.
• Added absolute minimum tutorial notebook.

v0.0.12

• Added proper handle for antibody name composed of just numbers.
• Added outputs overview document.
• Updated QC notebooks
• Updated job templates
• Removed deprecated code

v0.0.11

• Adds support for Cell Ranger 10x v2 5' (when SEQC outputs are not available).
• Uses quay.io/hisplan by default.
• Removes and use https://github.com/hisplan/docker-cutadapt instead.
• Uses seqc-utils:0.5.2.

v0.0.10

• Handles an edge case where doublets don't exist.
• Refactored for SCING.
• Uses seqc-utils:0.5.1.

v0.0.9

• Supports ASAP-seq.
• Generates AnnData for all assays.
• Updates the inspection scripts to use the generated AnnData.
• Changes the workflow name from Sharp to Hashtag
• Uses hto_gex_mapper to speed up the HTO <--> GEX translation process.
• Adds maxRetries: 3 to the workflow option file.
• Removed unnecessary input variables from CiteSeq and Preprocess.
• Adds unit tests

v0.0.8

• Refactored to support Amazon ECR.
• Renamed QC to SanityCheck.
• Removed sc.pp.calculate_qc_metrics from CITE-seq AnnData.

v0.0.7

• Added demuxMode for K-Means based demultiplexing: 1=default, 2=noisy methanol, 3=aggressively rescue from doublets
• Added minCount: total count for CB less than this threshold will be marked as negative (unreliable observations)
• Beta support for 10x Cell Multiplexing (aka. cellplex)

v0.0.6

• Auto-computes memory requirements if -1 is passed to Sharp.resourceSpec. This helps process 400M+ reads and/or 20K+ cells
• Refactored to support different versions of CITE-seq-Count.