• Check Design File for spaces in name and file contents
  • Update design example, README, and astrocyte.yml with current barcode IDs
  • Remove unnecessary intermediate process files
  • Add config option for running on AWS
  • Ignore dual index
  • Add parameter for base mask (not available in Astrocyte)
  • Output Nextflow version in QC report
  • Output pipeline version (manual) in QC report


  • Add Nextflow Tower integration into CI (GHH's profile)
  • Update to be runnable on cloud
  • Refactor configs

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
  • If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging