Version history

What’s Changed

See also the CHANGELOG.

New Contributors

Full Changelog: 2.7.1…3.0.0

What’s Changed

  • 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)

See also the CHANGELOG.

New Contributors

Full Changelog: 2.7.0…2.7.1

What’s Changed

New Contributors

Full Changelog: 2.6.0…2.7.0

What’s Changed

New Contributors

Full Changelog: 2.5.1…2.6.0

What’s Changed

Full Changelog: 2.5.0…2.5.1

What’s Changed

Full Changelog: https://github.com/nf-core/scrnaseq/blob/dev/CHANGELOG.md#v250---2024-01-02

What’s Changed

Full Changelog: 2.4.0…2.4.1

What’s Changed

  • 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.

New Contributors

This release is focused simply on ensuring as many containers as possible are hosted on quay.io.

What’s Changed

Full Changelog: 2.3.1…2.3.2

What’s Changed

New Contributors

Full Changelog: 2.3.0…2.3.1

Enhancements & fixes

  • Fix problem on samplesheet check related to amount of columns ([#211])
  • 211 samplesheet error in v220 when more than 3 fields are present by @fmalmeida in #216
  • Remove unused —bustools_correct and —skip_bustools and fix bugs in schema defaults by @drpatelh in #219
  • Fixed bug in starsolo output cardinality by @robsyme in #220

Full Changelog: 2.2.0…2.3.0

What’s Changed

See CHANGELOG.md

New Contributors

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

What’s Changed (detailed version)

New Contributors

Full Changelog: 2.0.0…2.1.0

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

What’s Changed

New Contributors

Full Changelog: 1.1.0…2.0.0

Several updates / fixes have been added, prior to converting the pipeline to DSLv2 and adding more advanced features.

  • 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 - 2019-12-09 “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