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scLR-multi: Changelog

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

[Unreleased]

Changed

  • Updated project metadata and documentation for the independent scLR-multi release.

v1.0.0 [2026-08-28]

Added

  • Extended support for multiple single-cell long-read RNA-seq technologies.
  • Added support for 10x Genomics 3' and 5' protocols, Parse Biosciences, and Argentag.
  • Added technology-specific preprocessing followed by a unified downstream analysis workflow.

Changed

  • Pipeline identity and documentation updated from nf-core/scnanoseq to scLR-multi.

Upstream nf-core/scnanoseq history

v1.2.1 [2025-09-02]

Fixes

  • Fixed issue where -resume would not always cache IsoQuant steps, resulting in silently skipping chromosomes

v1.2.0 [2025-06-09]

Enhancements

  • Fixed issue with linting.yml preventing automatic template PRs
  • Upgraded nf-core template to 3.2.1
  • Upgraded nanocomp nf-core module (no version change)
  • (nf-core#44) All output files produced by isoquant are now produced in the results file
  • (nf-core#45) Reference files are now accepted in .zip format
  • (nf-core#47) BLAZE scripts has been removed from the repo so the actual published code can be used
  • (nf-core#47) Added new whitelists for 10X 3v4 and 10X 5v3
  • (nf-core#56) Fixed an error where using --skip_dedup would end the pipeline early
  • (nf-core#58) Fixed UMI length for 5 prime chemistries
  • Fixed an error caused by --skip_qc and --skip_seurat
  • Seurat process now places the seurat object to pipeline outputs
  • No longer output uncorrected correct barcodes
  • Updated metro diagram

Software dependencies

Dependency Old version New version
BLAZE 2.2.0 2.5.1

v1.1.0 [2025-03-18]

Enhancements

  • Inputs for IsoQuant are split on chromosome to allow for faster processing
  • The read counts QC metric is now able to leverage NanoPlot counts if FastQC is skipped
  • Added oarfish as an option for quantification
  • Added picard markdupes as an option for deduplication

Fixes

  • The 'Post Trim Read QC' and 'Post Extract Read QC' nodes on the metro diagram have been placed in correct locations (closes issue #36)
  • The BLAZE process in the example config has been corrected to use cpus instead of --threads

Software dependencies

Dependency Old version New version
IsoQuant 3.5.0 3.6.1
MultiQC 1.25 1.25.1

v1.0.0 [2024-10-07]

Initial release of nf-core/scnanoseq, created with the nf-core template.