v1.2.0
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)
Background
- 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