name: create_gene_heatmap
description: Generate a gene count heatmap based on annotated and filtered gene counts data.
keywords:
  - bioinformatics tools
  - data visualization
  - gene heatmap
tools:
  - create_gene_heatmap:
      description: |
        The create_gene_heatmap module generates a heatmap of gene counts using ComplexHeatmap R package.
        It supports gene selection via additional files and provides a log-transformed visualization of the data.
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - annotated_endo_data:
        type: file
        description: |
          A tab-separated file containing  normalized expression counts for the Endogenous genes (genes as columns and samples as rows).
        pattern: "*.tsv"
    - normalized_counts:
        type: file
        description: |
          A tab-separated file containing normalized gene expression counts for all genes both Endogenous and Housekeeping genes, depending on the normalization method chosen (genes as rows and samples as columns).
        pattern: "*.tsv"
  - - heatmap_genes_to_filter:
        type: file
        description: |
          Optional Path to YAML file (list, one item per line) to specify which genes should be used for the gene-count heatmap.
output:
  - gene_heatmap:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*gene_heatmap_mqc.png":
          type: file
          description: |
            A PNG image containing the gene count heatmap, suitable for inclusion in MultiQC reports.
          pattern: "*gene_heatmap_mqc.png"
  - versions:
      - versions.yml:
          type: file
          description: File containing the software versions.
          pattern: "versions.yml"
authors:
  - "@apeltzer"
  - "@christopher-mohr"
maintainers:
  - "@nschcolnicov"
