User Facing

  • Add references to of tools to mutiQC report
  • Add BICF details to multiqc report
  • Create cellranger_count design file (if only 1 flowcell is inputted)


  • Add DOI (develop branch)
  • Add changelog as link to astrocyte docs (master branch)
  • Update example design file link in astrocyte docs (master branch)
  • Check tarballed bcl directory for spaces and exit if it contains one...cellranger mkfastq cannot handle spaces (develop branch)
  • Move untar (including space check) to bash script
  • Add Jeremy Mathews to author list
  • Apply style guide
  • Add pytests for ouptuts

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