The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Fix that cellranger workflow couldn't be run and enable CI for this workflow (#288).
- Update modules (#288nf-core#288).
- Update template to v2.11.1 (#279)
- Add support for paired GEX+ATAC sequencing using cellranger-arc (#274)
- Increase default runtime limits for some processes (#281, #284)
- Better support for custom protocols (#273).
- The universc protocol is now specified via the
--protocolflag - Any protocol specified is now passed to the respective aligner
- Added a section to the documentation
- The universc protocol is now specified via the
- Fix whitelist logic for dropseq (#267)
- Fix false-positive filename check in cellranger module (#261)
- Template update to v2.10 (#269)
- 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_ecrprofile (#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.
- Move containers for pipeline to quay.io (#233)
- Add
public_aws_ecrconfig for using the AWS mirror of containers where possible (#225)
- Fix problem on samplesheet check related to amount of columns ([#211])
- Fixed bug in starsolo output cardinality.
- Added support to output 10x count files in text format.
- Add gene symbols to count matrices
- Added UniverSC aligner to implement open-source version of Cell Ranger with wrapper for 40 technologies
- Update cellranger to v7.1.0 (#205).
- Autocanceling previous CI runs when new changes are pushed.
- Fixed #193 by updating the Seurat container directive
- Fixed #177 by adjusting the channels generation and usage when skipping fastqc
- Fixed #173 by adjusting parameter type and adding them to modules.config
- Fixed #170 by adding UniverSC subworkflow using new module
- Fixed #196 by adjusting runtime requirements for AlevinQC
- Fixed #191 by updating simpleAF containers to latest version
- Alevin workflow updated to use Alevin-Fry via simpleaf - thanks to @rob-p for supporting this and @fmalmeida implementing the support
- 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
- Pipeline ported to dsl2
- Template update with latest nf-core/tools v2.1
- Added cellranger v.7.0.0 subworkflow
- Added full size tests
- Make sure pipeline runs on multiple samples #77
- Fix issue where STARsolo always uses 10XV2 chemistry #60
- 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
Initial release of nf-core/scrnaseq, created with the nf-core template. This includes the following workflow options:
- Salmon Alevin + AlevinQC
- STARSolo
- Kallisto / BUStools