User Facing

  • Change Cellranger Version to 3.1.0
  • Fix countDesign to take multiple samples
  • Add MIT License
  • Check Design File for spaces in name and file contents
  • Update design example, README, and astrocyte.yml with current barcode IDs


  • Add CI artifacts
  • Add Nextflow Tower integration into CI (GHH's profile)

Known Bugs

  • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
    • note: 10x doesn't check github issues, emailed instead
    • note: pipeline checks for spaces and exits prematurely if found
  • If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
    • note: if multiple bcl files are detected then cellranger_count design file is not created