Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of scrnaseq

scrnaseq - 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 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

- Nextflow
Published by fmalmeida 12 months ago

scrnaseq - 3.0.0

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

- Nextflow
Published by grst about 1 year ago

scrnaseq - 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 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

- Nextflow
Published by grst over 1 year ago

scrnaseq - 2.7.0

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

- Nextflow
Published by grst over 1 year ago

scrnaseq - 2.6.0

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

- Nextflow
Published by grst almost 2 years ago

scrnaseq - 2.5.1

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

- Nextflow
Published by grst about 2 years ago

scrnaseq - nf-core/scrnaseq 2.5.0

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

- Nextflow
Published by grst about 2 years ago

scrnaseq - nf-core/scrnaseq 2.4.1

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

- Nextflow
Published by grst over 2 years ago

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

- Nextflow
Published by grst over 2 years ago

scrnaseq - 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 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

- Nextflow
Published by robsyme over 2 years ago

scrnaseq - 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 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

- Nextflow
Published by adamrtalbot over 2 years ago

scrnaseq - 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 https://github.com/nf-core/scrnaseq/pull/216
  • Remove unused --bustoolscorrect and --skipbustools 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

- Nextflow
Published by robsyme almost 3 years ago

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

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

- Nextflow
Published by grst almost 3 years ago

scrnaseq - 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 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(mtxtoseurat): 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

- Nextflow
Published by apeltzer over 3 years ago

scrnaseq - nf-core/scrnaseq V 2.0.0 "Gray Nickel Beagle"

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
  • transcriptomefasta -> transcriptfasta 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

- Nextflow
Published by apeltzer over 3 years ago

scrnaseq - nf-core/scrnaseq version 1.1.0 "Olive Mercury Corgi"

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

- Nextflow
Published by apeltzer almost 5 years ago

scrnaseq - nf-core/scrnaseq version 1.0.0 "Tiny Aluminium Crab" 2019-12-09

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

- Nextflow
Published by apeltzer about 6 years ago