pep_bio.yaml

pep_version: 2.0.0
sample_table: demo_sample_table.csv
sample_modifiers:
  append:
    Index: RG1
    pipeline_interfaces: pipeline_interface.yaml
  duplicate:
    read1: InputFile1
    read2: InputFile2
  derive:
    attributes: [read1, read2, Index, InputFile1, InputFile2]
    sources:
      FQ1: "data/{sample_name}_1.fq.gz"
      FQ2: "data/{sample_name}_2.fq.gz"
      RG1: "refgenie://{genome}/bwa_index"
  imply:
    - if: 
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
      then: 
        genome: t7
        prealignments: [t7, t7, t7]

refgenie:
  tag_overrides:
    t7:
      bowtie2_index: "alternative_tag"
  path_overrides:
    - registry_path: "hg19/bowtie2_index"
      value: "test.xyz"

looper:
  output_dir: pipeline_results
  compute:
    - "cores=5"
    - "mem=1500"

prealignments:
  - t7/bowtie2_index.dir:default
  - human_alu