YaqingLiu
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WesPipe
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Automated integrated analysis software for genomics data of the cancer patients.
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  1. {

  2.   "tumor_fastq_1": "",

  3.   "tumor_fastq_2": "",

  4.   "normal_fastq_1": "",

  5.   "normal_fastq_2": "",

  6.   "read_structure": "",

  7.   "duplex_umi": "",

  8.   "regions": "oss://ivd-product/reference/bed/Dynegene/SureSelectXT_HS_V8_S33266340_hg38_Regions.bed",

  9.   "interval_padding": "100",

  10.   "SENTIEON_LICENSE": "172.25.164.226:8990",

  11.   "fasta": "GRCh38_full_analysis_set_plus_decoy_hla.fa",

  12.   "ref_dir": "oss://ivd-product/reference/refGenome/",

  13.   "ref_flat": "oss://ivd-product/reference/refGenome/refFlat.hg38.txt",

  14.   "dbmills_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",

  15.   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",

  16.   "dbsnp": "dbsnp_146.hg38.vcf",

  17.   "dbsnp_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",

  18.   "annovar_database": "oss://genomics-platform-reference-data/annovar/",

  19.   "annotsv_database": "oss://ivd-product/reference/AnnotSV/",

  20.   "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",

  21.   "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",

  22.   "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",

  23.   "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",

  24.   "fastq_screen_conf": "oss://genomics-platform-reference-data/fastq_screen_reference/fastq_screen.conf",

  25.   "screen_ref_dir": "oss://genomics-platform-reference-data/fastq_screen_reference/",

  26.   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sentieon-genomics:v202112.05",

  27.   "varscan_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/varscan2:v2.4.3",

  28.   "manta_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/manta:1.6.0",

  29.   "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",

  30.   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",

  31.   "annotsv_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annotsv:3.1.3",

  32.   "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.9",

  33.   "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",

  34.   "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",

  35.   "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqscreen:0.12.0",

  36.   "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/fastqc:0.11.8",

  37.   "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/qualimap:2.0.0",

  38.   "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",

  39.   "cluster_16cpu_32gb": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

  40.   "cluster_2cpu_4gb": "OnDemand bcs.es.c.large img-ubuntu-vpc",

  41.   "disk_size": "500",

  42.   "qc": false,

  43.   "multi_caller": false

  44. }