example-params.json

{
  "study_id": "TEST-PR",
  "tumour_aln_analysis_id": "03905962-f1e1-41e8-9059-62f1e1c1e8fc",
  "normal_aln_analysis_id": "9940db0f-c100-496a-80db-0fc100d96ac1",
  "max_retries": 3,
  "first_retry_wait_time": 5,
  "cleanup": true,
  "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
  "score_url": "https://score.rdpc-qa.cancercollaboratory.org",
  "download": {
    "song_url": "https://song.rdpc-qa.cancercollaboratory.org",
    "song_cpus": 2,
    "song_mem": 2,
    "score_url": "https://score.rdpc-qa.cancercollaboratory.org",
    "score_cpus": 3,
    "score_mem": 8
  },
  "sangerWxsVariantCaller": {
    "cpus": 4,
    "mem": 10,
    "exclude": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr22,chrX,chrY,chrUn%,HLA%,%_alt,%_random,chrM,chrEBV",
    "vagrent_annot": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz",
    "ref_genome_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
    "ref_snv_indel_tar": "/nfs-dev-1-vol-qa-1/reference/sanger-variant-calling/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz"  
  },
  "generateBas": {
    "cpus":2,
    "mem":8,
    "ref_genome_fa": "/nfs-dev-1-vol-qa-1/reference/GRCh38_hla_decoy_ebv/GRCh38_hla_decoy_ebv.fa"
  },
  "repackSangerResults": {
    "cpus": 2,
    "mem": 4
  },
  "cavemanVcfFix": {
    "cpus": 2,
    "mem": 4
  },
  "prepSangerSupplement": {
    "cpus": 2,
    "mem": 4
  },
  "prepSangerQc": {
    "cpus": 2,
    "mem": 4
  },
  "extractSangerCall": {
    "cpus": 2,
    "mem": 4
  },
  "payloadGenVariantCall": {
    "cpus": 2,
    "mem": 4
  },
  "uploadVariant": {
    "cpus": 2,
    "mem": 4
  }
}