name: scvitools_solo
description: Detect doublets in single-cell RNA-Seq data
keywords:
  - scvi
  - solo
  - doublets
tools:
  - scvitools:
      description: "A scalable toolkit for probabilistic modeling applied to single-cell
        omics data"
      homepage: "https://scvi-tools.org"
      documentation: "https://docs.scvi-tools.org/en/stable/"
      tool_dev_url: "https://github.com/scverse/scvi-tools"
      licence:
        - "MIT"
      identifier: ""
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1' ]`
    - h5ad:
        type: file
        description: H5AD anndata object
        pattern: "*.h5ad"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5 format
  - batch_key:
      type: string
      description: Column in adata.obs to use as batch. If not provided, the entire dataset is treated as a single batch.
  - max_epochs:
      type: integer
      description: Maximum number of epochs to train the model. Defaults to the [heuristic default](https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.get_max_epochs_heuristic.html#scvi.model.get_max_epochs_heuristic).
output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - "*.h5ad":
          type: file
          description: H5AD anndata object without doublets
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590" # HDF5 format
  predictions:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - "*.pkl":
          type: file
          description: pandas dataframe containing the doublet classification
          pattern: "*.pkl"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
topics:
  versions:
    - versions.yml:
        type: string
        description: The name of the process
authors:
  - "@LeonHafner"
maintainers:
  - "@LeonHafner"
