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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.2.8] 2025-12

Added

    • Doublet detection functionality using Scrublet, with an optional flag to remove detected doublets from retained cells after two-step cell calling.
  • Mitochondrial percentage (pct_counts_mt) is added to adata.obs by default.

NOTE:

  • Metadata for doublet detection (Scrublet) and mitochondrial QC metrics are stored only when the input is an H5AD file.
  • For matrix-based (MTX) inputs (e.g. legacy alevin-fry outputs), doublet removal and mitochondrial QC plotting are supported; however, these metadata are not written to additional text files.

Modified

  • Extend .h5ad output support to mtx-based inputs, enabling QCatch to save both the full and filtered .h5ad files for all input types (MTX and .h5ad, simpleaf v0.19.5+).
  • For mtx-based input, save the intermediat results in .h5ad, No longer save to separate .txt files.

Fix

  • Logger set up.
  • gene-symbol name duplicates for write mtx-based h5ad

[0.2.7] 2025-11-04

Added

  • Support python 3.13.

Changed

  • Added automatic inference of the chemistry version from simpleaf quantification metadata.

  • Removed the default chemistry assumption — QCatch now requires either:

    1. a successfully inferred chemistry from simpleaf’s metadata,
    2. an explicitly specified chemistry via --chemistry (-c), or
    3. a custom number of partitions provided via --n_partitions (-n).

    If none of these are supplied, QCatch will stop and prompt the user to specify one.

[0.2.6] 2025-06-29

Added

  • Updated QCatch documentation and included an interactive demo page
  • Add tutorial scripts in the README.
  • Transitioned to uv for building and package management and relaxed dependencies for compatibility.

[0.2.5] 2025-05-19

Added

  • Adopted Cookiecutter-style structure based on the Scanpy project template.
  • Added a new flag to export summary metrics as a CSV file.
  • The HTML report now also includes a warning for low mapping rate.
  • Added unit tests and scripts to download test data
  • Updated the EmptyDrops step by removing the limitation on the number of candidate barcodes and making the FDR threshold dynamically adjustable based on the chemistry version.
  • Added source code snippets to the help text section of clustering plots

Changed

  • Switched to more concise progress logging during the cell-calling step.