peppro_output_schema.yaml

description: objects produced by PEPPRO pipeline.
properties:
  samples:
    type: array
    items:
      type: object
      properties:
        cutadapt_report: 
          path: "cutadapt/{sample_name}_cutadapt.txt"
          type: string
          description: "Test sample property"
        plus_bw: 
          path: "signal_{genome}/{sample_name}_plus_body_0-mer.bw"
          type: string
          description: "Test sample property"
        minus_bw: 
          path: "signal_{genome}/{sample_name}_minus_body_0-mer.bw"
          type: string
          description: "Test sample property"
        plus_bam: 
          path: "aligned_{genome}/{sample_name}_plus.bam"
          type: string
          description: "Test sample property"
        minus_bam: 
          path: "aligned_{genome}/{sample_name}_minus.bam"
          type: string
          description: "Test sample property"
        gene_counts_bed: 
          path: "signal_{genome}/{sample_name}_gene_coverage.bed"
          type: string
          description: "Test sample property"
        pause_indicies_bed: 
          path: "QC_{genome}/{sample_name}_pause_index.bed.gz"
          type: string
          description: "Test sample property"
  library_complexity_file:
    title: "Library complexity file"
    description: "Plots each sample's library complexity on a single plot."
    thumbnail_path: "summary/{name}_libComplexity.png"
    path: "summary/{name}_libComplexity.pdf"
    type: image
  counts_table:
    title: "Gene counts table"
    description: "Combines all sample gene count files into a project level gene counts table."
    path: "summary/{name}_countData.csv"
    type: link