v2.2.0
UserFacing
- Update cellranger to version 4.0.0
Background
- Add runtime info
- Make standard (profile) be biohpc AND cluster
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