renluyao
/
quartet-wgs-germline-qc
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quartet-wgs-germline-qc/inputs

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  1. {

  2.   "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",

  3.   "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",

  4.   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",

  5.   "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",

  6.   "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  7.   "{{ project_name }}.disk_size": "500",

  8.   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",

  9.   "{{ project_name }}.FASTQCdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",

  10.   "{{ project_name }}.project": "{{ project }}",

  11.   "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",

  12.   "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

  13.   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  14.   "{{ project_name }}.BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

  15.   "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",

  16.   "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",

  17.   "{{ project_name }}.FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",

  18.   "{{ project_name }}.SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  19.   "{{ project_name }}.QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",

  20.   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",

  21.   "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",

  22.   "{{ project_name }}.MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",

  23.   "{{ project_name }}.DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",

  24.   "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"

  25. }