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openpipelines-bio/openpipeline
Move components to separate packages

I was reviewing the components in this spreadsheet. I think I agree with all of the scopes listed in this PR, but would like to phase out certain components which would best be moved to a different location, ...
  • rcannood
  • Opened 
    10 days ago
  • #1029

openpipelines-bio/openpipeline
Add project and component metadata

Missing project metadata: - [ ] Descriptions - [ ] Useful links - [ ] Useful readme - ...? Missing component metadata: - [ ] Scope - [ ] Additional descriptions - [ ] How to use (readme ...
documentation
enhancement
urgent
  • rcannood
  • Opened 
    on Apr 25
  • #1011

openpipelines-bio/openpipeline
scGPT integration-based label transfer

workflows/annotation/scgpt_integration_knn was deprecated in OP 2.1.0 because: - zero-shot models are trained on gene names - gene names are not unique, causing issues when the query and reference ...
  • dorien-er
  • Opened 
    on Mar 14
  • #981

openpipelines-bio/openpipeline
Ingestion changes

At the end of each ingestion workflow, it would make sense if the output already contains some QC metrics and that the structure for this information is standardised across assay technologies. Currently, ...
enhancement
  • rcannood
  • Opened 
    on Feb 6
  • #965

openpipelines-bio/openpipeline
[Bug] Quality metrics get lost in the process_sample pipeline

cellranger_multi adds qc metrics to the output object, but these are removed in the process_sample pipeline This should be fixed in 2.0.0 but seems to be missing in production runs, to be added to the ...
  • ddemaeyer
  • 1
  • Opened 
    on Jan 28
  • #962

openpipelines-bio/openpipeline
Add disk space directive which scales with task attempts

We could create separate disk labels: withLabel: lowdisk { disk = { 20.GB * task.attempt } } withLabel: middisk { disk = { 50.GB * task.attempt } } withLabel: highdisk { disk = { 100.GB * task.attempt ...
bug
  • rcannood
  • Opened 
    on Nov 22, 2024
  • #905

openpipelines-bio/openpipeline
Gene cross-checking component

Implement general gene cross-checking component to account for feature overlap between reference and query data for downstream tasks
  • jakubmajercik
  • Opened 
    on Jul 10, 2024
  • #834

openpipelines-bio/openpipeline
SCANVI annotation component

Implement SCANVI component for scRNA-seq cell type annotation
  • jakubmajercik
  • Opened 
    on Jul 3, 2024
  • #826

openpipelines-bio/openpipeline
Pass target sum of counts per cell in normalize_total

Pass the target_sum argument is not being passed to sc.pp.normalize_total() in transform/normalize_total component and set default to None
  • jakubmajercik
  • Opened 
    on Jun 28, 2024
  • #822

openpipelines-bio/openpipeline
Implement CellTypist component

Implement CellTypist https://www.celltypist.org/ component for scRNA-seq cell type annotation
  • jakubmajercik
  • Opened 
    on Jun 14, 2024
  • #812
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