## 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 See also the [CHANGELOG](https://github.com/nf-core/scrnaseq/blob/master/CHANGELOG.md). ## 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

## What's Changed * Move `txp2gene` to `reference_genome_options` in schema as it is required by `kb_python` and `alevin` by @matq007 in https://github.com/nf-core/scrnaseq/pull/434 * Fix additional path splitting for `txp2gene` by @matq007 in https://github.com/nf-core/scrnaseq/pull/433 * Add a checker so that `--fb_reference` does not break the pipeline if `ab` files are not used in `cellranger multi` sub-workflow by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/410 * Fix concatenation of multiple samples into the combined output AnnData by @nictru in https://github.com/nf-core/scrnaseq/pull/416 * Ensure STARsolo velocity output is added to the combined output AnnData if `star_feature = 'Gene Velocyto'` by @nictru in https://github.com/nf-core/scrnaseq/pull/417 * Update cellbender module to latest nf-core version by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/419 * Add profile for GPU processes by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/419 * Update example usage command in README with valid reference genome parameter by @kopichris in https://github.com/nf-core/scrnaseq/pull/414 * Remove `--kb_filter` parameter, by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/422 * Improvements in `cellbender` documentation by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/423 * Add `--limitBAMsortRAM` to STARsolo alignment to ensure BAM sorting memory scales with task memory by @nictru in https://github.com/nf-core/scrnaseq/pull/430 * Replace local modules for `simpleaf`, `SIMPLEAF_INDEX`, and `SIMPLEAF_QUANT` with centralized nf-core modules, updating `simpleaf` sub-workflows accordingly by @DongzeHE in https://github.com/nf-core/scrnaseq/pull/424 * Update documentation for `simpleaf`, `alevin`, `salmon`, and `alevin-fry` for consistency by @DongzeHE in https://github.com/nf-core/scrnaseq/pull/424 * Rename the default aligner from `alevin` to `simpleaf` for consistency by @DongzeHE in https://github.com/nf-core/scrnaseq/pull/424 * Update `mtx_to_h5ad` template for `simpleaf` to use the h5ad file generated by `simpleaf` by @DongzeHE in https://github.com/nf-core/scrnaseq/pull/424 * Upgrade `alevinQC` from 1.12.1 to 1.18.0 to match the latest `simpleaf` output structure by @DongzeHE in https://github.com/nf-core/scrnaseq/pull/424 See also the [CHANGELOG](https://github.com/nf-core/scrnaseq/blob/master/CHANGELOG.md). ## New Contributors * @DongzeHE made their first contribution in https://github.com/nf-core/scrnaseq/pull/424 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/3.0.0...4.0.0

## What's Changed - Fix that tests have not been executed with nf-test v0.9 ([#359](https://github.com/nf-core/scrnaseq/pull/359)) - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348)) - Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350)) - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351)) - Fix resource specifications for `cellranger mkref`/`cellrangerarc mkref` ([#352](https://github.com/nf-core/scrnaseq/pull/352)) See also the [CHANGELOG](https://github.com/nf-core/scrnaseq/blob/master/CHANGELOG.md). ## New Contributors * @nick-youngblut made their first contribution in https://github.com/nf-core/scrnaseq/pull/348 * @eolaniru made their first contribution in https://github.com/nf-core/scrnaseq/pull/360 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/2.7.0...2.7.1

## What's Changed * Make it work without specifying GTF file by @grst in https://github.com/nf-core/scrnaseq/pull/322 * Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/328 * Adding cellrangermulti subworkflow by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/276 * Add `check_max` to AlevinQC time limit by @nictru in https://github.com/nf-core/scrnaseq/pull/335 * Bump version for v2.7 release by @grst in https://github.com/nf-core/scrnaseq/pull/325 * Include cellrangerarc in checker by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/337 * v2.7.0 release by @grst in https://github.com/nf-core/scrnaseq/pull/336 ## New Contributors * @nictru made their first contribution in https://github.com/nf-core/scrnaseq/pull/335 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/2.6.0...2.7.0

## What's Changed * Bump version to 2.6.0dev by @grst in https://github.com/nf-core/scrnaseq/pull/295 * Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/298 * Nf-test by @grst in https://github.com/nf-core/scrnaseq/pull/291 * Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/309 * kallisto|bustools 0.28.2 update by @gennadyFauna in https://github.com/nf-core/scrnaseq/pull/294 * Fix to issue 299 and 297 by @heylf in https://github.com/nf-core/scrnaseq/pull/300 * Fix issue 81, "call empty droplets" by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/301 * 316 update cellranger modules to latest nf coremodules versions by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/317 * Bump version to 2.6.0 by @grst in https://github.com/nf-core/scrnaseq/pull/320 * Add cellrangerarc snippet back by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/321 * Release v2.6.0 by @grst in https://github.com/nf-core/scrnaseq/pull/318 ## New Contributors * @gennadyFauna made their first contribution in https://github.com/nf-core/scrnaseq/pull/294 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/2.5.1...2.6.0

## What's Changed * Fix cellranger by @grst in https://github.com/nf-core/scrnaseq/pull/288 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/2.5.0...2.5.1

## What's Changed * Better support for custom chemistries by @grst in https://github.com/nf-core/scrnaseq/pull/273 * Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/279 * Adding cellranger-arc (multiome scRNA-seq + scATAC support) by @heylf in https://github.com/nf-core/scrnaseq/pull/274 * increase time limits by @grst in https://github.com/nf-core/scrnaseq/pull/281 * Fix time limits by @grst in https://github.com/nf-core/scrnaseq/pull/284 **Full Changelog**: https://github.com/nf-core/scrnaseq/blob/dev/CHANGELOG.md#v250---2024-01-02

## What's Changed * fix cellranger filename check by @grst in https://github.com/nf-core/scrnaseq/pull/261 * Fix 263 by @grst in https://github.com/nf-core/scrnaseq/pull/267 * Important! Template update for nf-core/tools v2.10 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/269 * Release v2.4.1 by @grst in https://github.com/nf-core/scrnaseq/pull/268 **Full Changelog**: https://github.com/nf-core/scrnaseq/compare/2.4.0...2.4.1