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HumanCellAtlas
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secondary-analysis
Secondary Analysis Service of the Human Cell Atlas Data Coordination Platform
https://pipelines.data.humancellatlas.org/ui/
BSD 3-Clause "New" or "Revised" License
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Complete HCA reference refactor work
#788
kbergin
closed
4 years ago
12
Move SS2 Pipeline Documentation to live near Pipeline
#787
kbergin
closed
4 years ago
5
Update DCP integration test for updating metadata
#786
kbergin
closed
5 years ago
1
Update integration test with pubsub changes
#785
samanehsan
closed
5 years ago
0
Analyze 10x KidneySingleCellAtlas dataset with Optimus in production
#784
kbergin
closed
5 years ago
10
Fix "unknown" analysis file types
#783
kbergin
closed
4 years ago
11
Move analysis related codes from various scattered places to `dcplib`
#782
kbergin
opened
5 years ago
1
Users can see the commands run on the data inside of a bam
#781
kbergin
opened
5 years ago
0
The notifier should be more friendly...
#780
rexwangcc
closed
5 years ago
0
Integrate EmptyDrops output in to the Optimus matrix result
#779
kbergin
closed
4 years ago
6
Use google pub/sub queue in Lira
#778
kbergin
closed
5 years ago
7
Standardize the access model of Terra Groups for HCA
#768
kbergin
opened
5 years ago
1
Explicitly raise errors when the bundle doesn't have enough metadata or info for us to process
#767
kbergin
closed
5 years ago
0
Capture Code Coverage Metrics
#766
rhiananthony
opened
5 years ago
3
Scientific validation of mouse reference for SS2
#765
kbergin
closed
5 years ago
1
H2 - Validate 3 Surge Pipelines
#764
kbergin
closed
4 years ago
0
Pipeline Testing
#763
kbergin
closed
4 years ago
0
Complete inDrops support in optimus
#762
kbergin
opened
5 years ago
0
Fix vulnerability in skylab requirements
#761
kbergin
closed
4 years ago
2
[Spike] Accelerate SplitBamByCellBarcode by splitting input into chunks
#760
kbergin
closed
5 years ago
0
Treat PAR_Y similarly to other large projects in HCA
#759
kbergin
opened
5 years ago
0
Incorporate additional metrics into SS2 outputs
#758
kbergin
opened
5 years ago
0
Smartseq2 Pipeline Backlog
#757
kbergin
opened
5 years ago
0
Scope scRNAseq Tertiary Pipeline for single dataset
#756
kbergin
closed
4 years ago
1
Scope plate based snRNAseq
#755
kbergin
opened
5 years ago
0
3' scRNAseq Chimeric Read Correction
#754
kbergin
opened
5 years ago
0
Scope DropSeq
#753
kbergin
opened
5 years ago
1
Pipeline Output UX in scRNA-seq
#752
kbergin
opened
5 years ago
0
GENCODE Gene IDs in Expression Matrices do not contain version information
#751
kbergin
opened
5 years ago
0
Fix ! workaround in zarr converter
#750
kbergin
opened
5 years ago
2
Query for 10x is too permissive
#749
kbergin
opened
5 years ago
5
Retry connection errors in cromwell tools
#748
kbergin
opened
5 years ago
0
Support Mouse data in HCA
#747
kbergin
closed
4 years ago
2
HCA references are in a more official location
#746
kbergin
closed
5 years ago
0
Move Lira scripts directory to secondary-analysis-deploy repo
#745
kbergin
opened
5 years ago
0
Drop the support for Python2
#744
kbergin
closed
4 years ago
2
Update Optimus adapter workflow's grouping of fastq reads
#743
kbergin
opened
5 years ago
3
Do not hard-code pipeline dependencies in mintegration test
#742
kbergin
closed
4 years ago
1
Ensure HCA datasets are analyzed in production
#741
kbergin
closed
5 years ago
14
Add maxRetries to HCA workflow options
#720
kbergin
closed
5 years ago
5
Q3 scATACseq pipeline work
#718
kbergin
closed
5 years ago
0
Update PR test data for Optimus
#706
kbergin
closed
5 years ago
15
Users can distinguish between tiers of pipelines in the HCA
#705
kbergin
closed
5 years ago
1
single cell: RNAVelocity
#698
kbergin
closed
5 years ago
0
max_retries instead of maxRetries in skylab
#696
kbergin
closed
5 years ago
0
Update Optimus in Terra with latest release
#688
kbergin
closed
5 years ago
6
Plate-based SS2
#686
kbergin
closed
5 years ago
0
Add support for SS2 Mouse
#674
kbergin
closed
4 years ago
6
Find a way to dump and aggregate the submission envelopes from our workflow logs! (HCA)
#672
kbergin
closed
5 years ago
0
Fix animal reference support for single-end SmartSeq2 pipeline
#670
kbergin
opened
5 years ago
1
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