default:
  raw_data_dir: "/data/proteomics/raw"
  processed_data_dir: "/data/proteomics/processed"
  sample_metadata: "/data/proteomics/metadata/samples.csv"

  normalization_method: "median"
  quantification: "LFQ"
  protein_fdr: 0.01

  differential_expression: true
  p_value_cutoff: 0.05

  plot:
    output_dir: "results/plots"
    format: "png"
    dpi: 300
