name: scvitools_scar
description: Module to use scAR to remove ambient RNA from single-cell RNA-seq data
keywords:
  - single-cell
  - scRNA-seq
  - ambient RNA removal
tools:
  - scvitools:
      description: scvi-tools (single-cell variational inference tools) is a package
        for end-to-end analysis of single-cell omics data
      documentation: https://docs.scvi-tools.org/en/stable/
      tool_dev_url: https://github.com/scverse/scvi-tools
      licence: ["BSD-3-clause"]
      identifier: ""
  - scar:
      description: scAR (single-cell Ambient Remover) is a deep learning model for removal
        of the ambient signals in droplet-based single cell omics.
      documentation: https://docs.scvi-tools.org/en/stable/user_guide/models/scar.html
      tool_dev_url: https://github.com/Novartis/scar
      licence: ["Novartis Terms of License"]
      identifier: biotools:scar
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - filtered:
        type: file
        description: AnnData file containing filtered data (without empty droplets)
        pattern: "*.h5ad"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5 format
    - unfiltered:
        type: file
        description: AnnData file containing unfiltered data (with empty droplets)
        pattern: "*.h5ad"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5 format
  - input_layer:
      type: string
      description: Layer to use as input. Defaults to `X`.
  - output_layer:
      type: string
      description: Layer to save the denoised counts to. Defaults to `scar`.
  - 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).
  - n_batch:
      type: integer
      description: Number of batches to use for generating the ambient profile. Defaults to 1. This can be increased to prevent out-of-memory errors.
output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.h5ad":
          type: file
          description: AnnData file containing decontaminated counts as `adata.X`
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590" # HDF5 format
  versions:
    - versions.yml:
        type: file
        description: File containing software version
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
topics:
  versions:
    - versions.yml:
        type: string
        description: The name of the process
authors:
  - "@nictru"
maintainers:
  - "@nictru"
