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

4.0.0

What's Changed

• Move txp2gene to reference_genome_options in schema as it is required by kb_python and alevin by @matq007 in #434
• Fix additional path splitting for txp2gene by @matq007 in #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 #410
• Fix concatenation of multiple samples into the combined output AnnData by @nictru in #416
• Ensure STARsolo velocity output is added to the combined output AnnData if star_feature = 'Gene Velocyto' by @nictru in #417
• Update cellbender module to latest nf-core version by @fmalmeida in #419
• Add profile for GPU processes by @fmalmeida in #419
• Update example usage command in README with valid reference genome parameter by @kopichris in #414
• Remove --kb_filter parameter, by @fmalmeida in #422
• Improvements in cellbender documentation by @fmalmeida in #423
• Add --limitBAMsortRAM to STARsolo alignment to ensure BAM sorting memory scales with task memory by @nictru in #430
• Replace local modules for simpleaf, SIMPLEAF_INDEX, and SIMPLEAF_QUANT with centralized nf-core modules, updating simpleaf sub-workflows accordingly by @DongzeHE in #424
• Update documentation for simpleaf, alevin, salmon, and alevin-fry for consistency by @DongzeHE in #424
• Rename the default aligner from alevin to simpleaf for consistency by @DongzeHE in #424
• Update mtx_to_h5ad template for simpleaf to use the h5ad file generated by simpleaf by @DongzeHE in #424
• Upgrade alevinQC from 1.12.1 to 1.18.0 to match the latest simpleaf output structure by @DongzeHE in #424

See also the CHANGELOG.

New Contributors

• @DongzeHE made their first contribution in #424

Full Changelog: 3.0.0...4.0.0

3.0.0

What's Changed

• Update doc related to simpleaf, alevin-fry and salmon. by @an-altosian in #368
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #381
• Fix gzip error by @esrice in #382
• Add pre-built indexes for Cellranger, Cellranger-arc, simpleaf and simpleaf txp2gene by @FelixKrueger in #390
• feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines by @kopichris in #387
• Standardize conversion workflow by @fmalmeida in #369
• Remove universc subworkflow from pipeline by @fmalmeida in #396
• Better readme statement by @apeltzer in #405
• include nac conversion workflow by @fmalmeida in #406

See also the CHANGELOG.

New Contributors

• @an-altosian made their first contribution in #368
• @esrice made their first contribution in #382
• @FelixKrueger made their first contribution in #390
• @kopichris made their first contribution in #387

Full Changelog: 2.7.1...3.0.0

2.7.1

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

• @nick-youngblut made their first contribution in #348
• @eolaniru made their first contribution in #360

Full Changelog: 2.7.0...2.7.1

2.7.0

What's Changed

• Make it work without specifying GTF file by @grst in #322
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #328
• Adding cellrangermulti subworkflow by @fmalmeida in #276
• Add check_max to AlevinQC time limit by @nictru in #335
• Bump version for v2.7 release by @grst in #325
• Include cellrangerarc in checker by @fmalmeida in #337
• v2.7.0 release by @grst in #336

New Contributors

• @nictru made their first contribution in #335

Full Changelog: 2.6.0...2.7.0

2.6.0

What's Changed

• Bump version to 2.6.0dev by @grst in #295
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #298
• Nf-test by @grst in #291
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #309
• kallisto|bustools 0.28.2 update by @gennadyFauna in #294
• Fix to issue 299 and 297 by @heylf in #300
• Fix issue 81, "call empty droplets" by @fmalmeida in #301
• 316 update cellranger modules to latest nf coremodules versions by @fmalmeida in #317
• Bump version to 2.6.0 by @grst in #320
• Add cellrangerarc snippet back by @fmalmeida in #321
• Release v2.6.0 by @grst in #318

New Contributors

• @gennadyFauna made their first contribution in #294

Full Changelog: 2.5.1...2.6.0

2.5.1

What's Changed

• Fix cellranger by @grst in #288

Full Changelog: 2.5.0...2.5.1

nf-core/scrnaseq 2.5.0

What's Changed

• Better support for custom chemistries by @grst in #273
• Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in #279
• Adding cellranger-arc (multiome scRNA-seq + scATAC support) by @heylf in #274
• increase time limits by @grst in #281
• Fix time limits by @grst in #284

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

nf-core/scrnaseq 2.4.1

What's Changed

• fix cellranger filename check by @grst in #261
• Fix 263 by @grst in #267
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #269
• Release v2.4.1 by @grst in #268

Full Changelog: 2.4.0...2.4.1

nf-core/scrnaseq 2.4.0 - "Lime Platinum Crab"

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

• @shinthor made their first contribution in #254