v2.1.5
UserFacing
- 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
Background
- 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