name: "scry_deviance"
description: Select highly deviant genes for integration using scry binomial deviance
keywords:
  - feature-selection
  - single-cell
  - scrnaseq
  - integration
tools:
  - "scry":
      description: "scry: Single-Cell RNA-Seq Analysis Utilities"
      homepage: "https://bioconductor.org/packages/scry"
      documentation: "https://bioconductor.org/packages/release/bioc/html/scry.html"
      tool_dev_url: "https://github.com/cole-trapnell-lab/scry"
      licence: ["GPL-3.0"]
      identifier: biotools:bioconductor-scry

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"
    - n_genes:
        type: integer
        description: |
          Number of highly deviant genes to retain. If 0, defaults to 4000.
    - excluded_genes:
        type: file
        description: |
          Optional file with one gene symbol per line to exclude before feature selection.
    - batch_col:
        type: string
        description: |
          Optional column in obs / colData for batch-aware deviance feature selection.

output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - "*.h5ad":
          type: file
          description: AnnData object subset to highly deviant genes
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590"
  var:
    - "*_features.csv":
        type: file
        description: CSV with binomial_deviance and highly_deviant columns per gene
        pattern: "*_features.csv"
        ontologies:
          - edam: "http://edamontology.org/format_3752"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750

authors:
  - "@nictru"
maintainers:
  - "@nictru"
containers:
  docker:
    linux/amd64:
      name: community.wave.seqera.io/library/scry_deviance:42e91d77e88fcfe6
      build_id: bd-42e91d77e88fcfe6_1
      scan_id: sc-a3305fea29b1e7b0_1
    linux/arm64:
      name: community.wave.seqera.io/library/scry_deviance:e6de94678d508788
      build_id: bd-e6de94678d508788_1
      scan_id: sc-fee203c32c2b4626_1
  singularity:
    linux/amd64:
      name: oras://community.wave.seqera.io/library/scry_deviance:5d41236dea2d0037
      build_id: bd-5d41236dea2d0037_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c4/c430d984a431d374c285a7a577f0496d8a514c1ad484feaaa86655259b594eb8/data
    linux/arm64:
      name: oras://community.wave.seqera.io/library/scry_deviance:fcc163e55be10858
      build_id: bd-fcc163e55be10858_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24af11b88761bc7c73f8047cc76358629cc63f527c9a206a885acb35bc49b717/data
  conda:
    linux/amd64:
      lock_file: modules/local/scry/deviance/.conda-lock/linux_amd64-bd-42e91d77e88fcfe6_1.txt
    linux/arm64:
      lock_file: modules/local/scry/deviance/.conda-lock/linux_arm64-bd-e6de94678d508788_1.txt
