# Custom Logo
custom_logo: 'bicf_logo.png'
custom_logo_url: 'https://www.utsouthwestern.edu/labs/bioinformatics/'
custom_logo_title: 'Bioinformatics Core Facility'

report_header_info:
    - Contact E-mail: 'bicf@utsouthwestern.edu'
    - Application Type: 'ChIP-seq'
    - Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
    - Contributors and Licensing: 'See https://doi.org/10.5281/zenodo.2648844'


# Title to use for the report.
title: BICF ChIP-seq Analysis Report

report_comment: >
  This report has been generated by the <a href="https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/" target="_blank">BICF/chipseq_analysis</a>
  pipeline.

extra_fn_clean_exts:
  - 'pbc.qc'
  - 'cc.qc'

fn_ignore_files:
  - '*dedup.flagstat.qc'

custom_data:
  library_complexity:
    file_format: 'tsv'
    id: 'library_complexity'
    contents: 'TotalReadPairs  DistinctReadPairs       OneReadPair     TwoReadPairs    NRF     PBC1    PBC2'
    section_name: 'Library complexity'
    plot_type: 'generalstats'
    pconfig:
        TotalReadPairs:
          decimalPlaces: 0
          shared_key: read_count
        DistinctReadPairs:
          decimalPlaces: 0
          shared_key: read_count
        NRF:
          decimalPlaces: 2
        PBC1:
          decimalPlaces: 2
        PBC2:
          decimalPlaces: 2

sp:
    phantompeakqualtools/out:
      fn: '*cc.qc'
    library_complexity:
      fn: '*pbc.qc'
    macs2:
      fn: '*_peaks.xls'


report_section_order:
    cutadapt:
      order: -1000
    Samtools:
      order: -1100
    Software_Versions:
      order: -1200
    Software_References:
      order: -1300

table_columns_placement:
    library_complexity:
      TotalReadPairs: 1100
      DistinctReadPairs: 1200
      NRF: 1300
      PBC1: 1400
      PBC2: 1500
    phantompeakqualtools:
      Estimated_Fragment_Length_bp: 1600
      NSC: 1700
      RSC: 1800

table_columns_visible:
  cutadapt:
    percent_trimmed: False
  library_complexity:
    OneReadPair: False
    TwoReadPairs: False

table_cond_formatting_rules:
    library_complexity_mqc-generalstats-library_complexity-NRF:
      pass:
        - gt: 0.8
      warn:
        - lt: 0.8
      fail:
        - lt: 0.5
    library_complexity_mqc-generalstats-library_complexity-PBC1:
      pass:
        - gt: 0.8
      warn:
        - lt: 0.8
      fail:
        - lt: 0.5
    library_complexity_mqc-generalstats-library_complexity-PBC2:
      pass:
        - gt: 3
      warn:
        - lt: 3
      fail:
        - lt: 1

thousandsSep_format: ''