name: cellbender_removebackground
description: Module to use CellBender to estimate 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' ]
    - h5ad:
        type: file
        description: AnnData file containing unfiltered data (with empty droplets)
        pattern: "*.h5ad"
        ontologies: []
output:
  h5:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}.h5:
          type: file
          description: Full count matrix as an h5 file, with background RNA
            removed. This file contains all the original droplet barcodes.
          pattern: "*.h5"
          ontologies: []
  filtered_h5:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}_filtered.h5:
          type: file
          description: |
            Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells.
          pattern: "*.h5"
          ontologies: []
  posterior_h5:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}_posterior.h5:
          type: file
          description: |
            The full posterior probability of noise counts. This is not normally used downstream.
          pattern: "*.h5"
          ontologies: []
  barcodes:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}_cell_barcodes.csv:
          type: file
          description: |
            CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. |
            Barcodes are written in plain text. This information is also contained in each of the above outputs, |
            but is included as a separate output for convenient use in certain downstream applications.
          pattern: "*.csv"
          ontologies:
            - edam: http://edamontology.org/format_3752 #CSV
  metrics:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}_metrics.csv:
          type: file
          description: |
            Metrics describing the run, potentially to be used to flag problematic runs |
            when using CellBender as part of a large-scale automated pipeline.
          pattern: "*.csv"
          ontologies:
            - edam: http://edamontology.org/format_3752 #CSV
  report:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}_report.html:
          type: file
          description: |
            HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings.
          pattern: "*.html"
          ontologies: []
  pdf:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}.pdf:
          type: file
          description: PDF file that provides a standard graphical summary of the
            inference procedure.
          pattern: "*.pdf"
          ontologies: []
  log:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ${prefix}.log:
          type: file
          description: Log file produced by the cellbender remove-background run.
          pattern: "*.log"
          ontologies: []
  checkpoint:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - ckpt.tar.gz:
          type: file
          description: Checkpoint file which contains the trained model and the
            full posterior.
          pattern: "*.ckpt"
          ontologies: []
  versions_cellbender:
    - - ${task.process}:
          type: string
          description: The name of the process
      - cellbender:
          type: string
          description: The name of the tool
      - cellbender --version:
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The name of the process
      - cellbender:
          type: string
          description: The name of the tool
      - cellbender --version:
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@nictru"
maintainers:
  - "@nictru"
