Published October 30, 2025 | Version 4.1.0
Software Open

nf-core/scrnaseq: 4.1.0

Authors/Creators

  • 1. University of Brasilia @compgenunb
  • 2. Boehringer Ingelheim
  • 3. @seanome
  • 4. Orakl Oncology
  • 5. Altos Labs
  • 6. Robert Bosch GmbH
  • 7. @seqeralabs
  • 8. @lifebit-ai
  • 9. Seqera Labs
  • 10. Fewsats
  • 11. Seqera
  • 12. @AgResearch Invermay
  • 13. Human Technopole
  • 14. Institute of Cancer Sciences, University of Glasgow
  • 15. National University of Singapore
  • 16. Altos Labs, Cambridge Institute of Science
  • 17. Arc Institute
  • 18. @ZS
  • 19. AstraZeneca India

Description

What's Changed

  • bumpt dev branch version by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/447
  • Json schema improvements by @abartlett004 in https://github.com/nf-core/scrnaseq/pull/453
  • Change simpleaf protocol name from 10xv4 to 10xv4-3p by @milos7250 in https://github.com/nf-core/scrnaseq/pull/452
  • updated --cellranger_index docs to point out that the base index directory is needed by @nick-youngblut in https://github.com/nf-core/scrnaseq/pull/458
  • Fix: Support for --aligner cellrangerarc by @matbonfanti in https://github.com/nf-core/scrnaseq/pull/441
  • Add ruff to pre-commit checks by @grst in https://github.com/nf-core/scrnaseq/pull/464
  • Update cellranger modules to use tool v9 by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/467
  • Fix refgenome error by @nictru in https://github.com/nf-core/scrnaseq/pull/469
  • Update protocol documentation by @nictru in https://github.com/nf-core/scrnaseq/pull/459
  • Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/466
  • Add the accelerator process directive to the process_gpu label co… by @stevekm in https://github.com/nf-core/scrnaseq/pull/477
  • Enable processing of on chip multiplexing sequence data by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/482
  • Implement skip_multiqc parameter available in nextflow.config by @Mridul-Chaudhary in https://github.com/nf-core/scrnaseq/pull/479
  • Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/474
  • Refactor iGenomes handling to expose params object pipeline-wide by @LeonHafner in https://github.com/nf-core/scrnaseq/pull/483
  • Fix nf test version by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/487
  • Bump version 4.1.0 for release by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/484
  • exclude conda profile by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/489
  • Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/496
  • Attempt to fix awsfulltest by @grst in https://github.com/nf-core/scrnaseq/pull/499
  • Release version 4.1.0 of pipeline by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/485

New Contributors

  • @abartlett004 made their first contribution in https://github.com/nf-core/scrnaseq/pull/453
  • @milos7250 made their first contribution in https://github.com/nf-core/scrnaseq/pull/452
  • @matbonfanti made their first contribution in https://github.com/nf-core/scrnaseq/pull/441
  • @stevekm made their first contribution in https://github.com/nf-core/scrnaseq/pull/477
  • @Mridul-Chaudhary made their first contribution in https://github.com/nf-core/scrnaseq/pull/479
  • @LeonHafner made their first contribution in https://github.com/nf-core/scrnaseq/pull/483

Full Changelog: https://github.com/nf-core/scrnaseq/compare/4.0.0...4.1.0

Files

nf-core/scrnaseq-4.1.0.zip

Files (28.2 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/scrnaseq/tree/4.1.0 (URL)

Software

Repository URL
https://github.com/nf-core/scrnaseq