{
    "fastp_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/fastp:0.19.6",
    "fastp_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "trim_front1": "0",
    "trim_tail1": "0",
    "max_len1": "0",
    "trim_front2": "0",
    "trim_tail2": "0",
    "max_len2": "0",
    "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
    "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
    "disable_adapter_trimming": "0",
    "length_required": "50",
    "length_required1": "20",
    "UMI": "0",
    "umi_len": "0",
    "umi_loc": "umi_loc",
    "qualified_quality_phred": "20",
    "disable_quality_filtering": "1",
    "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/hisat2:v2.1.0-2",
    "hisat2_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "idx_prefix": "genome_snp_tran",
    "idx": "oss://hcc1395/reference_genome/reference_RNAseq/reference/hisat2/grch38_snp_tran/",
    "pen_cansplice":"0",
    "pen_noncansplice":"12",
    "pen_noncansplice_unstrand":"3",
    "pen_intronlen":"G,-8,1",
    "min_intronlen":"20",
    "min_intronlen_unstrand":"30",
    "max_intronlen":"500000",
    "maxins":"500",
    "minins":"0",
    "samtools_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/samtools:v1.3.1",
    "samtools_cluster": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
    "insert_size":"8000",
    "gtf": "oss://hcc1395/reference_genome/reference_RNAseq/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
    "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/stringtie:v1.3.4",
    "stringtie_cluster": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
    "minimum_length_allowed_for_the_predicted_transcripts":"200",
    "minimum_isoform_abundance":"0.01",
    "Junctions_no_spliced_reads":"10",
    "maximum_fraction_of_muliplelocationmapped_reads":"0.95",
    "fastqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/fastqc:v0.11.5",
    "fastqc_disk_size": "150",
    "qualimapBAMqc_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/qualimap:2.0.0",
    "qualimapBAMqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "qualimapBAMqc_disk_size": "500",
    "qualimapRNAseq_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/qualimap:2.0.0",
    "qualimapRNAseq_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "qualimapRNAseq_disk_size": "500",
    "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/fastqscreen:0.12.0",
    "fastqscreen_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "screen_ref_dir": "oss://hcc1395/reference_genome/reference_RNAseq/fastq_screen_reference/",
    "fastq_screen_conf": "oss://hcc1395/reference_genome/reference_RNAseq/fastq_screen_reference/fastq_screen.conf",
    "disk_size": "200",
    "fastqscreen_disk_size": "200",
    "multiqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
    "multiqc_docker": "registry-vpc.cn-shanghai.aliyuncs.com/hcc1395_aliyun/multiqc:v1.8",
    "multiqc_disk_size": "100",
    "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/pgx-ballgown:0.0.1",
    "ballgown_cluster": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
    "strand_specific": false
}