Version history
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
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