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rnaseq-engineering
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  1. {

  2.   "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",

  3.   "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",

  4.   "idx_prefix": "genome_snp_tran",

  5.   "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

  6.   "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",

  7.   "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",

  8.   "fastqscreen_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

  9.   "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",

  10.   "fastqc_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

  11.   "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",

  12.   "fastp_cluster": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",

  13.   "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",

  14.   "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",

  15.   "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",

  16.   "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  17.   "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

  18.   "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  19.   "qualimap_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",

  20.   "qualimap_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  21.   "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",

  22.   "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  23.   "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",

  24.   "ballgown_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",

  25.   "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",

  26.   "count_cluster": "OnDemand bcs.ps.g.large img-ubuntu-vpc",

  27.   "insert_size":"8000",

  28.   "count_length": "150",

  29.   "trim_adapter": true,

  30.   "pre_alignment_qc": true,

  31.   "qualimap_qc": true

  32. }