What’s Changed

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

See also the CHANGELOG.

New Contributors

• @an-altosian made their first contribution in https://github.com/nf-core/scrnaseq/pull/368
• @esrice made their first contribution in https://github.com/nf-core/scrnaseq/pull/382
• @FelixKrueger made their first contribution in https://github.com/nf-core/scrnaseq/pull/390
• @kopichris made their first contribution in https://github.com/nf-core/scrnaseq/pull/387

Full Changelog: https://github.com/nf-core/scrnaseq/compare/2.7.1…3.0.0

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 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

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 https://github.com/nf-core/scrnaseq/pull/254

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 https://github.com/nf-core/scrnaseq/pull/233
• Dev -> Master for 2.3.2 release by @drpatelh in https://github.com/nf-core/scrnaseq/pull/234

Full Changelog: https://github.com/nf-core/scrnaseq/compare/2.3.1…2.3.2

What’s Changed

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

New Contributors

• @adamrtalbot made their first contribution in https://github.com/nf-core/scrnaseq/pull/225
• @stan0610 made their first contribution in https://github.com/nf-core/scrnaseq/pull/224

Full Changelog: https://github.com/nf-core/scrnaseq/compare/2.3.0…2.3.1

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 https://github.com/nf-core/scrnaseq/pull/216
• Remove unused —bustools_correct and —skip_bustools and fix bugs in schema defaults by @drpatelh in https://github.com/nf-core/scrnaseq/pull/219
• Fixed bug in starsolo output cardinality by @robsyme in https://github.com/nf-core/scrnaseq/pull/220

Full Changelog: https://github.com/nf-core/scrnaseq/compare/2.2.0…2.3.0

What’s Changed

See CHANGELOG.md

New Contributors

• @kafkasl made their first contribution in https://github.com/nf-core/scrnaseq/pull/163
• @ameynert made their first contribution in https://github.com/nf-core/scrnaseq/pull/164
• @Vivian-chen16 made their first contribution in https://github.com/nf-core/scrnaseq/pull/168
• @TomKellyGenetics made their first contribution in https://github.com/nf-core/scrnaseq/pull/185
• @azedine-healx made their first contribution in https://github.com/nf-core/scrnaseq/pull/202

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

New Contributors

• @drpatelh made their first contribution in https://github.com/nf-core/scrnaseq/pull/118
• @heylf made their first contribution in https://github.com/nf-core/scrnaseq/pull/121
• @mribeirodantas made their first contribution in https://github.com/nf-core/scrnaseq/pull/132
• @RHReynolds made their first contribution in https://github.com/nf-core/scrnaseq/pull/135
• @vjmarteau made their first contribution in https://github.com/nf-core/scrnaseq/pull/145
• @Khajidu made their first contribution in https://github.com/nf-core/scrnaseq/pull/148
• @robsyme made their first contribution in https://github.com/nf-core/scrnaseq/pull/144

Full Changelog: https://github.com/nf-core/scrnaseq/compare/2.0.0…2.1.0

v2.0.0 - 2022-06-17 “Gray Nickel Beagle”

• Pipeline ported to dsl2
• Template update with latest nf-core/tools v2.1
• Added cellranger v.7.0.0 subworkflow
• Added full size tests

Fixes

• Make sure pipeline runs on multiple samples #77
• Fix issue where STARsolo always uses 10XV2 chemistry #60

What’s Changed

• DSL2 version with working alevin workflow by @KevinMenden in https://github.com/nf-core/scrnaseq/pull/55
• Remove social preview image to use GitHub OpenGraph by @maxulysse in https://github.com/nf-core/scrnaseq/pull/57
• Added kallistobustools by @KevinMenden in https://github.com/nf-core/scrnaseq/pull/56
• Update to new file structure by @KevinMenden in https://github.com/nf-core/scrnaseq/pull/62
• Merge template update v2.1 by @ggabernet in https://github.com/nf-core/scrnaseq/pull/74
• DSL2 conversion by @ggabernet in https://github.com/nf-core/scrnaseq/pull/73
• Fix kallistobus didn’t run with multiple samples by @grst in https://github.com/nf-core/scrnaseq/pull/77
• Fix alevinqc by @grst in https://github.com/nf-core/scrnaseq/pull/79
• Important! Template update for nf-core/tools v2.2 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/76
• Update README.md by @medulka in https://github.com/nf-core/scrnaseq/pull/59
• Refactor workflows into subworkflows by @grst in https://github.com/nf-core/scrnaseq/pull/87
• Integrate cellranger workflow by @grst in https://github.com/nf-core/scrnaseq/pull/90
• Important! Template update for nf-core/tools v2.4 by @nf-core-bot in https://github.com/nf-core/scrnaseq/pull/101
• Fix Lint & Update latest modules by @apeltzer in https://github.com/nf-core/scrnaseq/pull/102
• Add AWS Full Size Tests by @apeltzer in https://github.com/nf-core/scrnaseq/pull/103
• Updating docs by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/104
• transcriptome_fasta -> transcript_fasta by @leipzig in https://github.com/nf-core/scrnaseq/pull/97
• AWS test all profiles and fix publishdir by @ggabernet in https://github.com/nf-core/scrnaseq/pull/106
• fix full test by @ggabernet in https://github.com/nf-core/scrnaseq/pull/107
• add default to outdir as it was in schema by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/108
• Fixes full tests with 10x references by @apeltzer in https://github.com/nf-core/scrnaseq/pull/109
• update CI and full size test by @ggabernet in https://github.com/nf-core/scrnaseq/pull/112
• Update nextflow.config by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/111
• Fix for STAR chemistry issue #60 by @apeltzer in https://github.com/nf-core/scrnaseq/pull/113
• PR for Release 2.0.0 by @fmalmeida in https://github.com/nf-core/scrnaseq/pull/105

New Contributors

• @ggabernet made their first contribution in https://github.com/nf-core/scrnaseq/pull/74
• @grst made their first contribution in https://github.com/nf-core/scrnaseq/pull/77
• @medulka made their first contribution in https://github.com/nf-core/scrnaseq/pull/59
• @fmalmeida made their first contribution in https://github.com/nf-core/scrnaseq/pull/104
• @leipzig made their first contribution in https://github.com/nf-core/scrnaseq/pull/97

Full Changelog: https://github.com/nf-core/scrnaseq/compare/1.1.0…2.0.0

Several updates / fixes have been added, prior to converting the pipeline to DSLv2 and adding more advanced features.

• Template update with latest nf-core/tools v1.13.2
• Parameters JSON Schema added #42
• 25 Fix small documentation error with wrong parameter for txp2gene

Fixes

• #20 Fix Transcriptome Fasta argument not detected well
• #21 Fix --kallisto_index being ignored

v1.0.0 - 2019-12-09 “Tiny Aluminium Crab”

Initial release of nf-core/scrnaseq, created with the nf-core template. This includes the following workflow options:

• Salmon Alevin + AlevinQC
• STARSolo
• Kallisto / BUStools