CHANGELOG.md

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