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RNAseq-qc-directional
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RNAseq-qc-directional/defaults

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  1. {   

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

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

  4.     "trim_front1": "0",

  5.     "trim_tail1": "0",

  6.     "max_len1": "0",

  7.     "trim_front2": "0",

  8.     "trim_tail2": "0",

  9.     "max_len2": "0",

  10.     "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",

  11.     "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",

  12.     "disable_adapter_trimming": "0",

  13.     "length_required": "50",

  14.     "length_required1": "20",

  15.     "UMI": "0",

  16.     "umi_len": "0",

  17.     "umi_loc": "umi_loc",

  18.     "qualified_quality_phred": "20",

  19.     "disable_quality_filtering": "1",

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

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

  22.     "idx_prefix": "genome_snp_tran",

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

  24.     "pen_cansplice":"0",

  25.     "pen_noncansplice":"12",

  26.     "pen_intronlen":"G,-8,1",

  27.     "min_intronlen":"20",

  28.     "max_intronlen":"500000",

  29.     "maxins":"500",

  30.     "minins":"0",

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

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

  33.     "insert_size":"8000",

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

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

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

  37.     "minimum_length_allowed_for_the_predicted_transcripts":"200",

  38.     "minimum_isoform_abundance":"0.01",

  39.     "Junctions_no_spliced_reads":"10",

  40.     "maximum_fraction_of_muliplelocationmapped_reads":"0.95",

  41.     "fastqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

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

  43.     "fastqc_disk_size": "150",

  44.     "qualimapBAMqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",

  45.     "qualimapBAMqc_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

  46.     "qualimapBAMqc_disk_size": "500",

  47.     "qualimapRNAseq_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",

  48.     "qualimapRNAseq_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

  49.     "qualimapRNAseq_disk_size": "500",

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

  51.     "fastqscreen_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

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

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

  54.     "fastqscreen_disk_size": "200",

  55.     "multiqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

  56.     "multiqc_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",

  57.     "multiqc_disk_size": "100",

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

  59.     "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"

  60.     }