name: "scran_normalization"
description: Compute scran size-factor normalisation and store log-normalised counts in an AnnData layer
keywords:
  - normalization
  - single-cell
  - scrnaseq
  - scran
tools:
  - "scran":
      description: "Methods for single-cell RNA-seq data analysis"
      homepage: "https://bioconductor.org/packages/scran/"
      documentation: "https://bioconductor.org/packages/release/bioc/html/scran.html"
      tool_dev_url: "https://github.com/libscran/scran"
      licence: ["GPL-3.0-or-later"]
      identifier: biotools:scran

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1' ]`
    - h5ad:
        type: file
        description: AnnData object in h5ad format with raw counts in `X` or a `counts` layer
        pattern: "*.{h5ad}"
        ontologies:
          - edam: "http://edamontology.org/format_3590"

output:
  h5ad:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      - "*.h5ad":
          type: file
          description: AnnData object with a `scran` layer
          pattern: "*.h5ad"
          ontologies:
            - edam: "http://edamontology.org/format_3590"
  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/arm64:
      name: community.wave.seqera.io/library/bioconductor-scran_bioconductor-scater_bioconductor-anndatar_bioconductor-singlecellexperiment_bioconductor-rhdf5:6b7470a8dda01c5a
      build_id: bd-6b7470a8dda01c5a_1
      scan_id: sc-725475b458007e58_1
    linux/amd64:
      name: community.wave.seqera.io/library/bioconductor-scran_bioconductor-scater_bioconductor-anndatar_bioconductor-singlecellexperiment_bioconductor-rhdf5:88502e87f79b51e8
      build_id: bd-88502e87f79b51e8_1
      scan_id: sc-5c65ff608ec1956a_1
  singularity:
    linux/arm64:
      name: oras://community.wave.seqera.io/library/bioconductor-scran_bioconductor-scater_bioconductor-anndatar_bioconductor-singlecellexperiment_bioconductor-rhdf5:096fc5b6f231bb68
      build_id: bd-096fc5b6f231bb68_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/1018024c31ecf24d8c52cf9db7610b043dd63053c91def87ab979d345b920330/data
    linux/amd64:
      name: oras://community.wave.seqera.io/library/bioconductor-scran_bioconductor-scater_bioconductor-anndatar_bioconductor-singlecellexperiment_bioconductor-rhdf5:9a526df3f432bd30
      build_id: bd-9a526df3f432bd30_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0b/0b2b49fe343301d4aa2eb471d77a86b7d20be65804b6dca5294b212594abd6b5/data
  conda:
    linux/amd64:
      lock_file: modules/local/scran/normalization/.conda-lock/linux_amd64-bd-88502e87f79b51e8_1.txt
    linux/arm64:
      lock_file: modules/local/scran/normalization/.conda-lock/linux_arm64-bd-6b7470a8dda01c5a_1.txt
