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

nf-core/scrnaseq v2.3.2 "Sepia Samarium Salmon"

This release is focused simply on ensuring as many containers as possible are hosted on quay.io.

What's Changed

• Move containers for pipeline to quay.io by @drpatelh in #233
• Dev -> Master for 2.3.2 release by @drpatelh in #234

Full Changelog: 2.3.1...2.3.2

nf-core/scrnaseq v2.3.1 "Yellow Strontium Pinscher"

What's Changed

• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in #221
• Public aws ecr profile by @adamrtalbot in #225
• Fix code comment by @stan0610 in #224
• Update docs for release 2.3.1 by @adamrtalbot in #227
• Remove globs from ecr profile by @adamrtalbot in #228
• Release candidate v2.3.1 by @adamrtalbot in #226

New Contributors

• @adamrtalbot made their first contribution in #225
• @stan0610 made their first contribution in #224

Full Changelog: 2.3.0...2.3.1