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nf-core/scrnaseq: Changelog

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

v2.3.2 - 2023-06-07 Patched Yellow Strontium Pinscher

  • Move containers for pipeline to quay.io (#233)

v2.3.1 - 2023-06-02 Yellow Strontium Pinscher

  • Add public_aws_ecr config for using the AWS mirror of containers where possible (#225)

v2.3.0 Steelblue Waspaloy Dachshund

  • Fix problem on samplesheet check related to amount of columns ([#211])
  • Fixed bug in starsolo output cardinality.

v2.2.0

  • Added support to output 10x count files in text format.
  • Add gene symbols to count matrices
  • Added UniverSC aligner to implement open-source version of Cell Ranger with wrapper for 40 technologies
  • Update cellranger to v7.1.0 (#205).

Fixes

  • Autocanceling previous CI runs when new changes are pushed.
  • Fixed #193 by updating the Seurat container directive
  • Fixed #177 by adjusting the channels generation and usage when skipping fastqc
  • Fixed #173 by adjusting parameter type and adding them to modules.config
  • Fixed #170 by adding UniverSC subworkflow using new module
  • Fixed #196 by adjusting runtime requirements for AlevinQC
  • Fixed #191 by updating simpleAF containers to latest version

v2.1.0 - 2022-10-06 "Green Mercury Siberian Husky"

  • Alevin workflow updated to use Alevin-Fry via simpleaf - thanks to @rob-p for supporting this and @fmalmeida implementing the support

Fixes

  • Fixed Kallistobustools workflow #123 by upgrading to nf-core/modules module
  • Fixed matrix conversion error when running STAR with --soloFeatures GeneFull #135
  • Fixed seurat matrix conversion error when running with conda profile #136
  • Fixed Kallistobustools module #116. By updating nf-core module and making sure conversion modules take into account the different outputs produced by kallisto standard and non-standard workflows.
  • Updated pipeline template to nf-core/tools 2.6

v2.0.0 - 2022-06-17 "Gray Nickel Beagle"

  • Pipeline ported to dsl2
  • Template update with latest nf-core/tools v2.1
  • Added cellranger v.7.0.0 subworkflow
  • Added full size tests

Fixes

  • Make sure pipeline runs on multiple samples #77
  • Fix issue where STARsolo always uses 10XV2 chemistry #60

v1.1.0 - 2021-03-24 "Olive Mercury Corgi"

  • Template update with latest nf-core/tools v1.13.2
  • Parameters JSON Schema added #42
  • 25 Fix small documentation error with wrong parameter for txp2gene

Fixes

  • #20 Fix Transcriptome Fasta argument not detected well
  • #21 Fix --kallisto_index being ignored

v1.0.0 - 2019-11-28 "Tiny Aluminium Crab"

Initial release of nf-core/scrnaseq, created with the nf-core template. This includes the following workflow options:

  • Salmon Alevin + AlevinQC
  • STARSolo
  • Kallisto / BUStools