nf-core/scrnaseq

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

10x-genomics10xgenomicsalevinbustoolscellrangerkallistorna-seqsingle-cellstar-solo

Launch version 4.1.0 https://github.com/nf-core/scrnaseq

Version history

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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.

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

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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.

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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