name: "edgepython_differential"
description: Run edgePython QL F-test on pseudobulk counts per cell-type stratum
keywords:
  - differential-expression
  - pseudobulk
  - edgepython
tools:
  - "edgepython":
      description: "Python implementation of edgeR-style differential expression"
      homepage: "https://github.com/pachterlab/edgePython"
      documentation: "https://github.com/pachterlab/edgePython"
      tool_dev_url: "https://github.com/pachterlab/edgePython"
      licence: ["GPL-3.0"]

input:
  - - meta:
        type: map
        description: Groovy Map containing sample information
    - h5ad:
        type: file
        description: Pseudobulk AnnData object in h5ad format
        pattern: "*.{h5ad}"
    - reference_condition:
        type: string
        description: Reference condition level for contrasts
    - interesting_genes:
        type: file
        description: Optional CSV of gene symbols to highlight on volcano plots
        pattern: "*.{csv,tsv,txt}"

output:
  results:
    - - meta:
          type: map
          description: Groovy Map containing sample information
      - "*_results.csv":
          type: file
          description: edgePython results per cell-type stratum
          pattern: "*_results.csv"
  plots:
    - "*.png":
        type: file
        description: Volcano plots for each contrast
        pattern: "*.png"
  multiqc_files:
    - "*_mqc.json":
        type: file
        description: MultiQC custom content for volcano plots
        pattern: "*_mqc.json"
  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/edgepython_differential:c767657d23bba8d5
      build_id: bd-c767657d23bba8d5_1
      scan_id: sc-a279fc2b81fe4f5d_1
    linux/amd64:
      name: community.wave.seqera.io/library/edgepython_differential:663a87cf9609bfbd
      build_id: bd-663a87cf9609bfbd_1
      scan_id: sc-e2ebd5c8773dfc24_1
  singularity:
    linux/arm64:
      name: oras://community.wave.seqera.io/library/edgepython_differential:1fdd708bb11aedb7
      build_id: bd-1fdd708bb11aedb7_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7f/7fd6b1b800c2ccdaa9eb5a908cfe729c3aab43cd1aa0266c66ea9659e4e30bf2/data
    linux/amd64:
      name: oras://community.wave.seqera.io/library/edgepython_differential:39de3eab444f7520
      build_id: bd-39de3eab444f7520_1
      https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dd/dd2bdd0dd3afef572c1ae41ca13cc1cd7a3e5ca62410c39934b10964ee916f71/data
  conda:
    linux/amd64:
      lock_file: modules/local/edgepython/differential/.conda-lock/linux_amd64-bd-663a87cf9609bfbd_1.txt
    linux/arm64:
      lock_file: modules/local/edgepython/differential/.conda-lock/linux_arm64-bd-c767657d23bba8d5_1.txt
