name: "scanorama_integrate"
description: Integrate single-cell batches with Scanorama
keywords:
  - integration
  - batch-correction
  - single-cell
tools:
  - "scanorama":
      description: "Batch correction and integration of single-cell datasets"
      homepage: "https://github.com/brianhie/scanorama"
      documentation: "https://github.com/brianhie/scanorama"
      tool_dev_url: "https://github.com/brianhie/scanorama"
      licence: ["MIT"]

input:
  - - meta:
        type: map
        description: Groovy Map containing sample information
    - h5ad:
        type: file
        description: AnnData object in h5ad format
        pattern: "*.{h5ad}"
    - batch_col:
        type: string
        description: obs column with batch labels
    - input_layer:
        type: string
        description: AnnData layer to read expression from (`X` or a layer name)
    - log_normalize:
        type: boolean
        description: When true, log-normalise counts from input_layer before integration; when false, use input_layer as pre-normalised expression

output:
  h5ad:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - "*.h5ad":
          type: file
          description: Integrated AnnData with Scanorama embedding in obsm
          pattern: "*.h5ad"
  obsm:
    - "X_*.pkl":
        type: file
        description: Integrated embedding as pickle
        pattern: "X_*.pkl"
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"

authors:
  - "@nictru"
maintainers:
  - "@nictru"
containers:
  docker:
    linux/arm64:
      name: community.wave.seqera.io/library/python_pyyaml_scanpy_scanorama:30d03381bfe6bb5f
      build_id: bd-30d03381bfe6bb5f_1
      scan_id: sc-8470978671cac67f_1
    linux/amd64:
      name: community.wave.seqera.io/library/python_pyyaml_scanpy_scanorama:095181a9ed452380
      build_id: bd-095181a9ed452380_1
      scan_id: sc-8b605a6e46a7adb7_1
  singularity:
    linux/arm64:
      name: oras://community.wave.seqera.io/library/python_pyyaml_scanpy_scanorama:7d72e3278e7e6862
      build_id: bd-7d72e3278e7e6862_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b3d9ee8d1211a7801cfce8fd6424ae9b093126e54a63df33a774edbd0ab34b9/data
    linux/amd64:
      name: oras://community.wave.seqera.io/library/python_pyyaml_scanpy_scanorama:622b4f6cf54e514a
      build_id: bd-622b4f6cf54e514a_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ee/ee5ffb0917263d09101dd05dc45c76aa239af97c58f2f5a368ac8a67a3eede3c/data
  conda:
    linux/amd64:
      lock_file: modules/local/scanorama/integrate/.conda-lock/linux_amd64-bd-095181a9ed452380_1.txt
    linux/arm64:
      lock_file: modules/local/scanorama/integrate/.conda-lock/linux_arm64-bd-30d03381bfe6bb5f_1.txt
