Scrnaseq Versions Save

A single-cell RNAseq pipeline for 10X genomics data

2.5.1

3 months ago

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

2.5.0

4 months ago

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

2.4.1

7 months ago

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

2.4.0

8 months ago

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

2.3.2

11 months ago

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

2.3.1

11 months ago

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

2.3.0

1 year ago

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

2.2.0

1 year ago

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

2.1.0

1 year ago

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

2.0.0

1 year ago

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