---
global:  # generall configs effecting one or multiple parts
  threads: 1
  assignments:
    split_number: 1  # number of files fastq should be split for parallelization
assignments:
  exampleAssignment:  # name of an example assignment (can be any string)
    bc_length: 15
    sequence_length:  # sequence length of design excluding adapters.
      min: 195
      max: 205
    alignment_start:  # start of an alignment in the reference. Here using 15 bp adapters. Can be different when using adapter free approaches
      min: 15  # integer
      max: 17  # integer
    min_mapping_quality: 1  # integer >=0 Please use 1 when you have oligos that differ by 1 base in your reference/design file
    FW:
      - resources/Assignment_BasiC/R1.fastq.gz
    BC:
      - resources/Assignment_BasiC/R2.fastq.gz
    REV:
      - resources/Assignment_BasiC/R3.fastq.gz
    reference: resources/design.fa
    configs:
      exampleAssignmentConfig:  # name of an example filtering config
        min_support: 3
        fraction: 0.7
experiments:
  exampleCount:
    bc_length: 15
    umi_length: 10
    data_folder: resources/Count_Basic/data
    experiment_file: resources/example_experiment.csv
    demultiplex: false
    assignments:
      fromFile:
        type: file
        assignment_file: resources/SRR10800986_filtered_coords_to_barcodes.tsv.gz
      fromWorkflow:
        type: config
        assignment_name: exampleAssignment
        assignment_config: exampleAssignmentConfig
    design_file: resources/design.fa
    label_file: resources/labels.tsv  # optional
    configs:
      exampleConfig:
        filter:
          bc_threshold: 10
          DNA:
            min_counts: 1
          RNA:
            min_counts: 1
        sampling:  # optional, just for benmarking
          DNA:
            total: 30000000
            threshold: 300
          RNA:
            total: 50000000
            threshold: 300
    variants:  # optional
      map: resources/variant_map.tsv
      min_barcodes: [5, 10]  # min BC for ref and alt sequence
