How to define a project

1. Start with a basic PEP

To start, you need a project defined in the standard Portable Encapsulated Project (PEP) format. Start by creating a PEP.

2. Specify the Sample Annotation

This information generally lives in a project_config.yaml file.

Simplest example:

pep_version: 2.0.0
sample_table: sample_annotation.csv

A more complicated example taken from PEPATAC:

pep_version: 2.0.0
sample_table: tutorial.csv

    attributes: [read1, read2]
      # Obtain tutorial data from 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"
    - if: 
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
        genome: hg38
        prealignment_names: ["rCRSd"]
        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: None     # Default. Use an external reference set of peaks instead of the peaks called from this run