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Recent Releases of https://github.com/alexslemonade/openscpca-nf

https://github.com/alexslemonade/openscpca-nf - v0.1.5

What's Changed

  • Default release date for ScPCA data is set to 2025-06-30
  • Update scpcaTools images to v0.4.3 versions
  • One new module:
    • infercnv-gene-order: Produce gene order files that can be used as input to inferCNV
  • Two modules have been updated:
    • merge-sce:
    • Two bugs were fixed:
      • The cell_id column in the merged object colData slot is now correctly formatted as {library id}-{barcode}
      • Merged object colData slots now include consensus cell type annotations in columns consensus_celltype_annotation and consensus_celltype_ontology
    • cell-type-ewings:
    • A bug causing some cells to be incorrectly classified was fixed

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.4...v0.1.5

- R
Published by sjspielman 11 months ago

https://github.com/alexslemonade/openscpca-nf - v0.1.5

What's Changed

  • Default release date for ScPCA data is set to 2025-06-30
  • Update scpcaTools images to v0.4.3 versions
  • One new module has been added:
    • infercnv-gene-order-file: Produce gene order files that can be used as input to inferCNV
  • Two modules have been updated:
    • merge-sce:
    • Two bugs were fixed:
      • The cell_id column in the merged object colData slot is now correctly formatted as {library id}-{barcode}
      • Merged object colData slots now include consensus cell type annotations in columns consensus_celltype_annotation and consensus_celltype_ontology
    • cell-type-ewings:
    • A bug causing some cells to be incorrectly classified was fixed

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.4...v0.1.5

- R
Published by sjspielman 11 months ago

https://github.com/alexslemonade/openscpca-nf - v0.1.4

What's Changed

  • Default release date for ScPCA data is set to 2025-03-20
  • One new module:
    • cell-type-ewings: Assigns cell types to Ewing sarcoma samples in SCPCP000015
  • One module as been updated:
    • cell-type-consensus:
    • Now uses the consensus cell type reference from OpenScPCA-analysis:v0.2.2
    • Exports gene expression for a set of marker genes in addition to assigned consensus cell types

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.3...v0.1.4

- R
Published by allyhawkins over 1 year ago

https://github.com/alexslemonade/openscpca-nf - v0.1.3

What's Changed

  • Two new modules:
    • seurat-conversion: converts processed SingleCellExperiment objects to Seurat objects
    • cell-type-consensus: assigns consensus cell type labels
  • Default release date for ScPCA data is set to 2024-11-25
  • A nextflow_schema.json file defining all workflow parameters is now available
    • Parameters are also validated as part of the main workflow
  • The testing profile can now be used for local testing of the workflow

New Contributors

  • @allyhawkins made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-nf/pull/113

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.2...v0.1.3

- R
Published by allyhawkins over 1 year ago

https://github.com/alexslemonade/openscpca-nf - v0.1.2

What's Changed

  • Update generated AnnData to match scpca-nf 0.8.5
  • Update simulation scripts to use new age columns
  • Update metadata in simulations to include project-specific fields
  • Mask any tokens in logs

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.1...v0.1.2

- R
Published by jashapiro over 1 year ago

https://github.com/alexslemonade/openscpca-nf - v0.1.1

What's Changed

  • Increase default memory for run_scdblfinder in https://github.com/AlexsLemonade/OpenScPCA-nf/pull/82

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-nf/compare/v0.1.0...v0.1.1

- R
Published by jashapiro almost 2 years ago

https://github.com/alexslemonade/openscpca-nf - v0.1.0 Initial release

  • Initial versioned release of the OpenScPCA-nf Nextflow workflow
  • Current modules:
    • example: a very small test module for testing configuration parameters
    • simulate-sce: creates simulated and permuted data for testing here and in OpenScPCA-analysis
    • merge-sce: merges multiple datasets into a single SCE object and corresponding AnnData objects
    • doublet-detection: runs scDblFinder to detect doublets in a dataset
  • The default workflow entrypoint currently runs the merge-sce and doublet-detection modules. Other workflow entrypoints are:
    • test to run the example module
    • simulate to run the simulate-sce module
  • Includes scripts for running the workflow on AWS batch through Code Deploy

- R
Published by jashapiro almost 2 years ago