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