Evidence collection
publish_2.2.0-evidences-89.json 6047b2c2
Collected 4 years ago
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
Evidence collection
publish_2.1.5-evidences-61.json f3cbaeab
Collected 4 years ago
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
Evidence collection
publish_1.3.1-evidences-50.json 8d326d8a
Collected 4 years ago
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
Evidence collection
publish_1.2.0-evidences-49.json 22643a62
Collected 4 years ago
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
Evidence collection
publish_1.1.4-evidences-48.json ea6a5e68
Collected 4 years ago
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
Evidence collection
publish_1.0.0-evidences-47.json afd056e3
Collected 4 years ago
Initial Astrocyte deployed version