example-params.json

{
  "study_id": "TEST-PR",
  "tumour_aln_analysis_id": "23cfc3c6-115d-4563-8fc3-c6115d9563d2",
  "normal_aln_analysis_id": "ce2a49b2-2bda-4ded-aa49-b22bdaadedb3",

  "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
  "score_url": "https://score.rdpc-qa.cancercollaboratory.org",

  "publish_dir": "",
  "max_retries": 3,
  "first_retry_wait_time": 5,

  "perform_bqsr": false,

  "ref_fa": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa",
  "mutect2_scatter_interval_files": "/nfs-dev-1-vol-qa-1/reference/gatk-resources/mutect2.scatter_by_chr/chr*.interval_list",
  "germline_resource_vcfs": [
    "/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.hg38.vcf.gz"
  ],
  "panel_of_normals": "/nfs-dev-1-vol-qa-1/reference/gatk-resources/1000g_pon.hg38.vcf.gz",
  "contamination_variants": "/nfs-dev-1-vol-qa-1/reference/gatk-resources/af-only-gnomad.pass-only.biallelic.snp.hg38.vcf.gz",

  "mem": 40,
  "cpus": 8
}