HumanCellAtlas / secondary-analysis

Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform

https://pipelines.data.humancellatlas.org/ui/

HumanCellAtlas/secondary-analysis Issues

Update the Optimus mouse data test to use the current testing style
Updated 4 years ago
Create a workflow test for Optimus using the dsde-pipelines workflow test infrastructure
Updated 4 years ago2
Optimize attachBarcodes in sctools
Updated 4 years ago
Optimus file outputs are not unique
Closed 4 years ago
Scope Tertiary for one dataset
Updated 4 years ago
Move HCA pipelines to WDL 1.0
Closed 4 years ago7
[SPIKE] AUDR: Analysis Updates reloaded
Updated 5 years ago1
Exclude 10x v3 datasets that have feature barcodes from the subscription query
Updated 5 years ago1
Analyze 10x 1M Neurons mouse dataset with Optimus in production
Updated 5 years ago2
[SPIKE] Optimus based snRNA-Seq pipeline for 10X V2/V3 chemistry
Closed 5 years ago2
Validate HCA SS2 pipeline for single-end read samples
Closed 5 years ago4
[HCA] Upgrade node pool machine type
Closed 5 years ago3
Investigate "None"s in Optimus metrics output
Closed 5 years ago2
Post-mortem analysis of the 2019/11/02 DCP 8k scaling test and investigation on the Kubernetes auto-scaler configuration
Closed 5 years ago7
Update Falcon logic to handle duplicate bundles
Updated 5 years ago
Backfill Optimus workflows with new input hash
Closed 5 years ago7
Add new content to Ss2 documentation
Closed 5 years ago
Analyze human 10x v3 dataset: scRNAseqSystemicComparison
Updated 5 years ago1
Investigate latency when Lira publishes messages to pubsub queue
Closed 5 years ago5
Analyze human 10x v3 dataset: HDCA-Sweden-10x
Updated 5 years ago
Validate HCA SS2 pipeline for Fluidigm samples
Closed 5 years ago13
Analysis mouse SS2 dataset: Tabula Muris
Updated 5 years ago1
Update 10x subscription query
Closed 5 years ago10
Update adapters for Optimus to reflect the fact that the chemistry of the data is V2
Closed 5 years ago11
Update Optimus query to accept 10x v2 or v3 data
Closed 5 years ago2
Analyze mouse 10x v2 dataset: Mouse Endoderm Project
Updated 5 years ago5
Create Changelog md for Optimus Pipeline
Closed 5 years ago1
Analyze mouse 10x and SS2 mouse data: scRNAseqSystemicComparison
Closed 5 years ago1
Fix and Update HCA Grafana dashboard for analysis service
Closed 5 years ago6
Analyze scRNAseqSystemicComparison dataset
Closed 5 years ago5
Finish TissueStability dataset
Closed 5 years ago2
Debug Lira/PubSub and improve Lira's logging
Closed 5 years ago3
Analyze mouse SS2 dataset: Mouse Melanoma
Updated 5 years ago1
Cut release of Optimus with 10X V3 support
Closed 5 years ago2
HCA DCP Data Tracker needs to know if a project violated the GDPR is erased or not.
Closed 5 years ago2
Update Optimus Documentation to reflect mouse and new output changes.
Closed 5 years ago5
Wipe all data from spatio-temporal kidney project
Closed 5 years ago4
Analyze mouse 10x v2 dataset: HumanColonicMesenchymeIBD
Closed 5 years ago6
Migrate lira's subscription service over to JMESPath
Updated 5 years ago
Clean up of Secondary Analysis Repo
Closed 5 years ago2
Check that the Optimus V3 is comparable to the outputs obtained by Cellranger
Closed 5 years ago9
Refactor Optimus Parameterization with respect to input chemistry
Closed 5 years ago5
AttachBarcodes V3 Code Path is Tested
Closed 5 years ago7
Improve manually starting HCA workflows
Closed 5 years ago1
Add PR tests for Optimus 10X scRNAseq V3 path in the pipeline
Closed 5 years ago1
testInfra
Closed 5 years ago
Analyze 10x v2 SingleCellLiverLandscape Dataset
Closed 5 years ago3
Analyze human 10X V2 dataset: Reprogrammed_Dendritic_Cells
Closed 5 years ago1
Make a dataset for PR validation of Optimus V3
Closed 5 years ago3
Refactor AttachBarcodes
Updated 5 years ago