# v2.2.0-indev
**User Facing**
* Add cellranger version 4.0.0
* Add references version 2020-A (GRCh38, mm10, mix)

**Background**

*Known Bugs*
* Vizapp does not yet work for Astrocyte
* Running in CLI: to set --fastq path of file/s needs to be in quotes


# v2.1.1
**User Facing**
* Check Design File for spaces in name and file contents
* Attempt to prevent thredding error (which appears to only happen on 256GBv1 nodes)
* Add option for 5' GEX chemistry
* Remove cellranger 3.0.1 as an option
* Fix CLI MultiQC failure bug

**Background**
* Add Nextflow Tower integration into CI (GHH's profile)
* Add new layered config folders, including prepare for awsifying
* Update param to new standard
* Update CI
* Add pipeline tracking tool

*Known Bugs*
* Vizapp does not yet work for Astrocyte
* Running in CLI: to set --fastq path of file/s needs to be in quotes

# v1.2.0
**User Facing**
* Add Cellranger Version 3.1.0
* Add human/mouse farmyard reference Version 3.1.0 from 10x
* Add Vizapp (shiny)
* Fix mutiqc error
* Add MIT License

**Background**
* Add CI Artifacts

*Known Bugs*
* Vizapp does not yet work for Astrocyte

# v1.1.0
**User Facing**
* Make report (multiqc) for cellranger qc output, version, references

**Background**
* Add changelog
* Add check for space in genomeLocationFull (cellranger cannot handle) in bash script
* Move module loads to process setup level code
* Add Jeremy Mathews to author list
* Apply style guide
* Add pytests for ouptuts
* Test for incompatible params (kitVersion=3 AND version=2.1.1)

*Known Bugs*