pep_schema.yaml

description: bedstat PEP schema

properties:
  samples:
    type: array
    items:
      type: object
      properties:
        sample_name: 
          type: string
          description: "name of the sample, which is the name of the output BED file"
        input_file_path:
          type: string
          description: "absolute path the file to convert"
        output_file_path:
          type: string
          description: "absolute path the file to the output BED file (derived attribute)"
        genome:
          type: string
          description: "organism genome code"
          enum: ["hg18", "hg19", "hg38", "mm9", "mm10"]
        narrowpeak:
          type: integer
          minimum: 0
          maximum: 1
          description: "binary number indicating whether the regions are narrow (transcription factor implies narrow, histone mark implies broad peaks)"
        format:
          type: string
          description: "file format"
          enum: ["bigWig", "bigBed", "bed", "wig", "bedGraph"]
        cell_type:
          type: string
          description: "cell type code"
        antibody:
          type: string
          description: "antibody used if ChIP-seq experiment"
        description:
          type: string
          description: "freeform description of the sample"
        exp_protocol:
          type: string
          description: "type of the experiment the file was generated in"
        data_source:
          type: string
          description: "source of the sample, preferably a GSE* code"
        treatment:
          type: string
          description: "freeform description of the sample treatment"
      required:
        - output_file_path
        - genome
        - sample_name
required:
  - samples