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

v1.3.1

User Facing

• Change Cellranger Version to 3.1.0
• Fix countDesign to take multiple samples
• Add MIT License
• Check Design File for spaces in name and file contents
• Update design example, README, and astrocyte.yml with current barcode IDs

Background

• Add CI artifacts
• Add Nextflow Tower integration into CI (GHH's profile)

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

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

v1.1.4

User Facing

• Fix design file not visible in Astrocyte
• Fix handling of multiple flowcells in 1 submission

Background

• Move multiqc config to conf folder
• Add CI test for multiple flowcells
• Add changelog
• Quote design/tarball/$baseDir path in processes in case of spaces

Known Bugs

• cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31

Initial Astrocyte deployed version