Releases: nf-core/scrnaseq
Releases · nf-core/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 #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
Contributors
robsyme, fmalmeida, and drpatelh
Assets 2
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
Contributors
kafkasl, TomKellyGenetics, and 3 other contributors
Assets 2
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_H5ADconversion 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
Contributors
robsyme, rob-p, and 9 other contributors
Assets 2
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 #55
- Remove social preview image to use GitHub OpenGraph by @maxulysse in #57
- Added kallistobustools by @KevinMenden in #56
- Update to new file structure by @KevinMenden in #62
- Merge template update v2.1 by @ggabernet in #74
- DSL2 conversion by @ggabernet in #73
- Fix kallistobus didn't run with multiple samples by @grst in #77
- Fix alevinqc by @grst in #79
- Important! Template update for nf-core/tools v2.2 by @nf-core-bot in #76
- Update README.md by @medulka in #59
- Refactor workflows into subworkflows by @grst in #87
- Integrate cellranger workflow by @grst in #90
- Important! Template update for nf-core/tools v2.4 by @nf-core-bot in #101
- Fix Lint & Update latest modules by @apeltzer in #102
- Add AWS Full Size Tests by @apeltzer in #103
- Updating docs by @fmalmeida in #104
- transcriptome_fasta -> transcript_fasta by @leipzig in #97
- AWS test all profiles and fix publishdir by @ggabernet in #106
- fix full test by @ggabernet in #107
- add default to outdir as it was in schema by @fmalmeida in #108
- Fixes full tests with 10x references by @apeltzer in #109
- update CI and full size test by @ggabernet in #112
- Update nextflow.config by @fmalmeida in #111
- Fix for STAR chemistry issue #60 by @apeltzer in #113
- PR for Release 2.0.0 by @fmalmeida in #105
New Contributors
- @ggabernet made their first contribution in #74
- @grst made their first contribution in #77
- @medulka made their first contribution in #59
- @fmalmeida made their first contribution in #104
- @leipzig made their first contribution in #97
Full Changelog: 1.1.0...2.0.0
Contributors
leipzig, maxulysse, and 7 other contributors
Assets 2
nf-core/scrnaseq version 1.1.0 "Olive Mercury Corgi"
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