name: "scdblfinder"
description: Detect doublets in single-cell RNA-seq data using scDblFinder
keywords:
  - doublet-detection
  - single-cell
  - scrnaseq
  - quality-control
tools:
  - "scdblfinder":
      description: "scDblFinder: Computational identification of doublets in single-cell transcriptomics data"
      homepage: "https://bioconductor.org/packages/scDblFinder"
      documentation: "https://bioconductor.org/packages/release/bioc/vignettes/scDblFinder/inst/doc/scDblFinder.html"
      tool_dev_url: "https://github.com/plger/scDblFinder"
      doi: "10.12688/f1000research.73600.2"
      licence: ["GPL-3.0"]
      identifier: biotools:scdblfinder

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1' ]`
    - h5ad:
        type: file
        description: AnnData object in h5ad format
        pattern: "*.{h5ad}"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5 format
    - dbr:
        type: number
        description: |
          Optional expected doublet rate (0-1). If null, scDblFinder estimates
          the doublet rate internally.
    - batch_col:
        type: string
        description: |
          Optional column in the AnnData obs / SingleCellExperiment colData used
          to split cells by capture or batch via scDblFinder's samples argument.

output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - "*.h5ad":
          type: file
          description: AnnData object with doublet annotations
          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' ]`
      - "*.csv":
          type: file
          description: CSV file containing doublet predictions (boolean)
          pattern: "*.csv"
          ontologies:
            - edam: "http://edamontology.org/format_3752" # CSV
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML

authors:
  - "@KurayiChawatama"
maintainers:
  - "@KurayiChawatama"
