How to specify a set of reference peaks

PEPATAC automatically calls peaks and will report the fraction of reads in peaks (FRiP) for that set of peaks. You may also specify a set of reference peaks and report the fraction of reads in those reference peaks. To do so, simply point the pipeline to your set of reference peaks, either at the command line using --frip-ref-peaks /path/to/your_reference_peaks.bed, or in a PEP configuration file like so:

name: PEPATAC_tutorial

pep_version: 2.0.0
sample_table: tutorial.csv

looper:
  output_dir: "${TUTORIAL}/processed/"
  pipeline_interfaces: ["${TUTORIAL}/tools/pepatac/project_pipeline_interface.yaml"]

sample_modifiers:
  append:
    pipeline_interfaces: ["${TUTORIAL}/tools/pepatac/sample_pipeline_interface.yaml"]
  derive:
    attributes: [read1, read2]
    sources:
      # Obtain tutorial data from http://big.databio.org/pepatac/ then set
      # path to your local saved files
      R1: "${TUTORIAL}/tools/pepatac/examples/data/{sample_name}_r1.fastq.gz"
      R2: "${TUTORIAL}/tools/pepatac/examples/data/{sample_name}_r2.fastq.gz"
  imply:
    - if:
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
      then:
        genome: hg38
        macs_genome_size: hs
        prealignments: rCRSd human_repeats
        deduplicator: samblaster # Default. [options: picard]
        trimmer: skewer          # Default. [options: pyadapt, trimmomatic]
        peak_type: fixed         # Default. [options: variable]
        extend: "250"            # Default. For fixed-width peaks, extend this distance up- and down-stream.
        frip_ref_peaks: /path/to/your_reference_peaks.bed