NGS Data QC

Implementation of the ngs_data_qc step

Default Configuration

The default configuration is as follows.

step_config:
  ngs_data_qc:

    # Override data set configuration search paths for FASTQ files
    #path_link_in: ''
    #tools:                                            # Options: 'fastqc', 'picard'
    #  - fastqc
    #  - picard
    #picard:
    #  path_ngs_mapping: ../ngs_mapping
    #
    #  # Required when CollectHsMetrics is among the programs
    #  path_to_baits: ''
    #
    #  # When missing, same as baits
    #  path_to_targets: ''
    #
    #  # Exon enrichment kit name (optional)
    #  bait_name: ''
    #  programs:                                       # REQUIRED
    #fastqc: {}