YaqingLiu
/
WesPipe
Bevaka 1
Stjärnmärk 0
Förgrening 0
Kod Ärenden 0 Pull-förfrågningar 0 Släpp 0 Wiki Aktiviteter
Automated integrated analysis software for genomics data of the cancer patients.
Du kan inte välja fler än 25 ämnen Ämnen måste starta med en bokstav eller siffra, kan innehålla bindestreck ('-') och vara max 35 tecken långa.
29 Incheckningar
1 Gren
Träd: 554d15de78
Grenar Taggar
${ item.name }
Skapa branchen ${ searchTerm }
från '554d15de78'
${ noResults }
WesPipe/defaults

36 lines
2.1KB
Rå Blame Historik 

  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": "0",

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

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

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

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

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

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

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

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

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

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

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

  35.   "disk_size": "200"

  36. }