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

v2.3.0 - 2023-05-03 Steelblue Waspaloy Dachshund

Enhancements & fixes

• Fix problem on samplesheet check related to amount of columns ([#211])
• 211 samplesheet error in v220 when more than 3 fields are present by @fmalmeida in #216
• Remove unused --bustools_correct and --skip_bustools and fix bugs in schema defaults by @drpatelh in #219
• Fixed bug in starsolo output cardinality by @robsyme in #220

Full Changelog: 2.2.0...2.3.0

nf-core/scrnaseq v2.2.0 "Titanium Chuckwalla"

What's Changed

See CHANGELOG.md

New Contributors

• @kafkasl made their first contribution in #163
• @ameynert made their first contribution in #164
• @Vivian-chen16 made their first contribution in #168
• @TomKellyGenetics made their first contribution in #185
• @azedine-healx made their first contribution in #202

nf-core/scrnaseq V 2.1.0 "Gray Nickel Beagle" Latest

v2.1.0 - 2022-10-06 "Green Mercury Siberian Husky"

• Alevin workflow updated to use Alevin-Fry via simpleaf - thanks to @rob-p for supporting this and @fmalmeida implementing the support

Fixes

• Fixed Kallistobustools workflow #123 by upgrading to nf-core/modules module
• Fixed matrix conversion error when running STAR with --soloFeatures GeneFull #135
• Fixed seurat matrix conversion error when running with conda profile #136
• Fixed Kallistobustools module #116. By updating nf-core module and making sure conversion modules take into account the different outputs produced by kallisto standard and non-standard workflows.
• Updated pipeline template to nf-core/tools 2.6

What's Changed (detailed version)

• Bump version dev by @apeltzer in #114
• Add mimetype to input parameter in schema by @drpatelh in #118
• Addition of MTX_TO_H5AD conversion modules by @fmalmeida in #117
• Dev - Adding FastQC to the pipeline, with integration into MultiQC by @heylf in #121
• Add seurat conversion by @fmalmeida in #125
• KBTools update to nf-core module by @apeltzer in #126
• fixing paths after kallisto update by @fmalmeida in #127
• PR: kallisto fix by @fmalmeida in #131
• Fix README shields / zenodo info by @mribeirodantas in #132
• fix: STAR mtx conversion when using GeneFull by @RHReynolds in #135
• fix(mtx_to_seurat): could not find ReadMtx using conda profile by @RHReynolds in #136
• Parse kallisto non-standard (spliced and unspliced) outputs by @fmalmeida in #133
• FIX: add "else if" instead of if-if by @fmalmeida in #140
• Important! Template update for nf-core/tools v2.5.1 by @nf-core-bot in #143
• Add def for print_error function by @vjmarteau in #145
• Repair inconsistency by @Khajidu in #148
• repair inconsistency by @Khajidu in #149
• Important! Template update for nf-core/tools v2.6 by @nf-core-bot in #151
• Switch from alevin to alevin-fry (with simpleaf) by @fmalmeida in #139
• Enable iGenomes by @robsyme in #144
• Release PR 2.1.0 by @apeltzer in #154

New Contributors

• @drpatelh made their first contribution in #118
• @heylf made their first contribution in #121
• @mribeirodantas made their first contribution in #132
• @RHReynolds made their first contribution in #135
• @vjmarteau made their first contribution in #145
• @Khajidu made their first contribution in #148
• @robsyme made their first contribution in #144

Full Changelog: 2.0.0...2.1.0