4.1.0

What's Changed

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

See also the CHANGELOG.

New Contributors

• @abartlett004 made their first contribution in #453
• @milos7250 made their first contribution in #452
• @matbonfanti made their first contribution in #441
• @stevekm made their first contribution in #477
• @Mridul-Chaudhary made their first contribution in #479
• @LeonHafner made their first contribution in #483

Full Changelog: 4.0.0...4.1.0