name: "decoupler_pseudobulk"
description: Aggregate single-cell counts into pseudobulk profiles with decoupler
keywords:
  - pseudobulk
  - differential-expression
  - single-cell
tools:
  - "decoupler":
      description: "Python package to perform enrichment and pseudobulk analysis from omics data"
      homepage: "https://decoupler.readthedocs.io/"
      documentation: "https://decoupler.readthedocs.io/"
      tool_dev_url: "https://github.com/saezlab/decoupler-py"
      licence: ["GPL-3.0"]

input:
  - - meta:
        type: map
        description: Groovy Map containing sample information
    - h5ad:
        type: file
        description: AnnData object in h5ad format
        pattern: "*.{h5ad}"
    - counts_layer:
        type: string
        description: Layer containing raw counts, or X
    - donor_col:
        type: string
        description: obs column with biological replicate identifiers
    - celltype_col:
        type: string
        description: obs column with cell type or cluster labels
    - condition_col:
        type: string
        description: obs column with condition labels
    - min_num_cells:
        type: integer
        description: Minimum cells per pseudobulk sample
    - min_total_counts:
        type: integer
        description: Minimum total counts per pseudobulk sample

output:
  h5ad:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - "*.h5ad":
          type: file
          description: Pseudobulk AnnData with counts in X
          pattern: "*.h5ad"
  samples:
    - "*_samples.tsv":
        type: file
        description: Pseudobulk sample metadata table
        pattern: "*_samples.tsv"
  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/decoupler_pseudobulk:3544cf5bf51a67eb
      build_id: bd-3544cf5bf51a67eb_1
      scan_id: sc-eb92c0c0e41dc466_1
    linux/amd64:
      name: community.wave.seqera.io/library/decoupler_pseudobulk:22ffb587b73301b8
      build_id: bd-22ffb587b73301b8_1
      scan_id: sc-ca4d1973b28013f7_1
  singularity:
    linux/amd64:
      name: oras://community.wave.seqera.io/library/decoupler_pseudobulk:ad376bac82cefac9
      build_id: bd-ad376bac82cefac9_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63b778907daa8743d21b65174088943b8ea7cb6efaa79605c2bf2ba0b61d2a84/data
    linux/arm64:
      name: oras://community.wave.seqera.io/library/decoupler_pseudobulk:b0b7d806f5ed5995
      build_id: bd-b0b7d806f5ed5995_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1a/1a40e20f344b704397d43636a86d0e89b6098406da4c72a15e9ed89c2bf07438/data
  conda:
    linux/amd64:
      lock_file: modules/local/decoupler/pseudobulk/.conda-lock/linux_amd64-bd-22ffb587b73301b8_1.txt
    linux/arm64:
      lock_file: modules/local/decoupler/pseudobulk/.conda-lock/linux_arm64-bd-3544cf5bf51a67eb_1.txt
