RNAseq_Variant_Calling/inputs

{
  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
  "{{ project_name }}.PIdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.18.2",
  "{{ project_name }}.platform": "ILLUMINA",
  "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  "{{ project_name }}.disk_size": "{{ disk_size }}",
  "{{ project_name }}.SAdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/star:2.7.0",
  "{{ project_name }}.fastq_1": "{{ read1 }}",
  "{{ project_name }}.machine": "{{ machine }}",
  "{{ project_name }}.STdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
  "{{ project_name }}.library": "{{ library }}",
  "{{ project_name }}.fastq_2": "{{ read2 }}",
  "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
  "{{ project_name }}.SAref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38_2.7.0d/",
  "{{ project_name }}.SAMdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
  "{{ project_name }}.STref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/",
  "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
  "{{ project_name }}.sample": "{{ sample }}",
  "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
  "{{ project_name }}.id": "{{ id }}",
  "{{ project_name }}.GATKdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01"
}