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nf-core/scrnaseq: Changelog

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

v2.7.1 - 2024-08-13

  • Fix that tests have not been executed with nf-test v0.9 (#359)
  • Add support for 10XV4 chemistry (#348)
  • Fix issues with predefined STAR index (#350)
  • Update modules (#351)
  • Fix resource specifications for cellranger mkref/cellrangerarc mkref (#352)

v2.7.0 - 2024-06-03

  • Apply check_max to AlevinQC time limit (#335)
  • Update template to v2.14.1 (#328)
  • Avoid filename collisions in cellranger-arc (#321)
  • Add cellranger multi subworkflow (#247)
    • Add support for 10x multiplexed, multi-omics and FFPE samples
    • Allow the use of gzipped fasta and GTF files
  • Fix that pipeline couldn't run without GTF file, even when an aligner index was specified (#322)

v2.6.0 - 2024-04-16

  • Update cellranger to v8.0.0 (#317)
  • Change from pytests to nf-test (#291)
  • Update template to v2.13.1 (#309)
  • Update to kallisto|bustools v0.28.2 (#294)
  • Fix cellrangerarc matrix conversions and protocol selection (#300)
  • Add new emptydrops calling module (#301)
  • Update cellranger modules to latest version ([#316])

v2.5.1 - 2024-01-23

  • Template update to v2.12 (#298).
  • Fix that cellranger workflow couldn't be run and enable CI for this workflow (#288).
  • Update modules (#288#288).

v2.5.0 - 2024-01-02

  • Update template to v2.11.1 (#279)
  • Add support for paired GEX+ATAC sequencing using cellranger-arc (#274)
  • Increase default runtime limits for some processes (#281, #284)
  • Better support for custom protocols (#273).
    • The universc protocol is now specified via the --protocol flag
    • Any protocol specified is now passed to the respective aligner
    • Added a section to the documentation

v2.4.1 - 2023-09-28

  • Fix whitelist logic for dropseq (#267)
  • Fix false-positive filename check in cellranger module (#261)
  • Template update to v2.10 (#269)

v2.4.0 - 2023-08-16 Lime Platinum Crab

  • Fix typo causing empty version imformation for mtx_conversion subworkflow (#254)
  • Add singularity.registry = 'quay.io' and bump NF version to 23.04.0 (#237)
  • Fixed issue with file collisions while using cellranger (#232)
  • Fix issue where multiqc inputs tried to access objects that did not exist (#239)
  • Removed public_aws_ecr profile (#242)
  • Include cellranger in MultiQC report (#244)
  • Nf-core template update to v2.9 (#245)
  • Update cellranger and fastqc module (#246). The updated cellranger module now automatically renames input FASTQ files to match the expected naming conventions.

v2.3.2 - 2023-06-07 Sepia Samarium Salmon

  • 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