name: cellbender_merge
description: Module to use CellBender to remove ambient RNA from single-cell
  RNA-seq data
keywords:
  - single-cell
  - scRNA-seq
  - ambient RNA removal
tools:
  - cellbender:
      description: CellBender is a software package for eliminating technical
        artifacts from high-throughput single-cell RNA sequencing (scRNA-seq)
        data.
      documentation: https://cellbender.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/broadinstitute/CellBender
      licence:
        - "BSD-3-Clause"
      identifier: biotools:CellBender
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: []
    - unfiltered:
        type: file
        description: AnnData file containing unfiltered data (with empty droplets)
        pattern: "*.h5ad"
        ontologies: []
    - cellbender_h5:
        type: file
        description: CellBender h5 file containing ambient RNA estimates
        pattern: "*.h5"
        ontologies: []
  - output_layer_name:
      type: string
      description: The name of the layer to store counts
output:
  h5ad:
    - - meta:
          type: file
          description: AnnData file containing decontaminated counts as `adata.X`
          pattern: "*.h5ad"
          ontologies: []
      - ${prefix}.h5ad:
          type: file
          description: AnnData file containing decontaminated counts as `adata.X`
          pattern: "*.h5ad"
          ontologies: []
  versions_cellbender:
    - versions.yml:
        type: file
        description: File containing software version
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750
topics:
  versions:
    - versions.yml:
        type: file
        description: File containing software version
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750
authors:
  - "@nictru"
maintainers:
  - "@nictru"
