# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: scanpy_scrublet
description: Detect doublets in single-cell RNA-seq data using Scrublet via Scanpy
keywords:
  - scrublet
  - doublet-detection
  - scanpy
  - single-cell
tools:
  - scanpy:
      description: Single-Cell Analysis in Python
      homepage: https://scanpy.readthedocs.io
      documentation: https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.scrublet.html
      tool_dev_url: https://github.com/scverse/scanpy
      doi: 10.1186/s13059-017-1382-0
      licence: ["BSD-3-Clause"]
      identifier: biotools:scanpy

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - h5ad:
        type: file
        description: AnnData object in h5ad format
        pattern: "*.{h5ad}"
        ontologies:
          - edam: "http://edamontology.org/format_3590" # HDF5 format
  - batch_col:
      type: string
      description: |
        Optional column name in adata.obs containing batch information
        If provided and contains multiple batches, will be used as batch_key parameter

output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.h5ad":
          type: file
          description: AnnData object with doublets removed
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590" # HDF5 format
  predictions:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*.pkl":
          type: file
          description: Pickle file containing doublet predictions
          pattern: "*.pkl"
          ontologies:
            - edam: "http://edamontology.org/format_3553" # Pickle format
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"

        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@nictru"
maintainers:
  - "@nictru"
