WesPipe/defaults

{
  "tumor_fastq_1": "",
  "tumor_fastq_2": "",
  "normal_fastq_1": "",
  "normal_fastq_2": "",
  "read_structure": "",
  "duplex_umi": "",
  "regions": "oss://ivd-product/reference/bed/Dynegene/SureSelectXT_HS_V8_S33266340_hg38_Regions.bed",
  "interval_padding": "100",
  "SENTIEON_LICENSE": "172.25.164.226:8990",
  "fasta": "GRCh38_full_analysis_set_plus_decoy_hla.fa",
  "ref_dir": "oss://ivd-product/reference/refGenome/",
  "ref_flat": "oss://ivd-product/reference/refGenome/refFlat.hg38.txt",
  "dbmills_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",
  "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
  "dbsnp": "dbsnp_146.hg38.vcf",
  "dbsnp_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",
  "annovar_database": "oss://genomics-platform-reference-data/annovar/",
  "annotsv_database": "oss://ivd-product/reference/AnnotSV/",
  "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
  "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
  "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",
  "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",
  "fastq_screen_conf": "oss://genomics-platform-reference-data/fastq_screen_reference/fastq_screen.conf",
  "screen_ref_dir": "oss://genomics-platform-reference-data/fastq_screen_reference/",
  "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sentieon-genomics:v202112.05",
  "varscan_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/varscan2:v2.4.3",
  "manta_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/manta:1.6.0",
  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",
  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",
  "annotsv_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annotsv:3.1.3",
  "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.9",
  "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",
  "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",
  "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqscreen:0.12.0",
  "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqc:0.11.8",
  "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/qualimap:2.0.0",
  "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",
  "cluster_16cpu_32gb": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
  "cluster_2cpu_4gb": "OnDemand bcs.es.c.large img-ubuntu-vpc",
  "disk_size": "500",
  "qc": false,
  "multi_caller": false
}