etc/gatk-wdl/cnv_somatic_pair_workflow.b38.inputs.json

   1 {
   2   "CNVSomaticPairWorkflow.normal_bam": "/share/FGI2017B/users/huxs/nsfcG/wgs/cnv2/WGS-Normal.hg38.bam",
   3   "CNVSomaticPairWorkflow.normal_bam_idx": "/share/FGI2017B/users/huxs/nsfcG/wgs/cnv2/WGS-Normal.hg38.bai",
   4   "CNVSomaticPairWorkflow.tumor_bam": "/share/FGI2017B/users/huxs/nsfcG/wgs/cnv2/WGS-B7B.hg38.bam",
   5   "CNVSomaticPairWorkflow.tumor_bam_idx": "/share/FGI2017B/users/huxs/nsfcG/wgs/cnv2/WGS-B7B.hg38.bai",
   6
   7   "CNVSomaticPairWorkflow.ref_fasta": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta",
   8   "CNVSomaticPairWorkflow.ref_fasta_fai": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.fasta.fai",
   9   "CNVSomaticPairWorkflow.ref_fasta_dict": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/Homo_sapiens_assembly38.dict",
  10   "CNVSomaticPairWorkflow.common_sites": "/share/FGI2017B/pub/gatk-data/gatk-test-data/cnv/somatic/hg38.common_snps.interval_list",
  11   "CNVSomaticPairWorkflow.read_count_pon": "/share/FGI2017B/users/huxs/nsfcG/wgs/cnv/WGS-Normal.pon.hdf5",
  12   "CNVSomaticPairWorkflow.intervals": "/ldfssz1/FGI/CCS/huxuesong/nsfcG/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
  13
  14
  15   "CNVSomaticPairWorkflow.gatk_docker": "broadinstitute/gatk:4.1.4.0",
  16   "##CNVSomaticPairWorkflow.gatk4_jar_override": "/share/FGI2017B/brew/Cellar/gatk/4.0.11.0/gatk-package-4.0.11.0-local.jar",
  17
  18   "CNVSomaticPairWorkflow.is_run_funcotator": "false",
  19   "##CNVSomaticPairWorkflow.is_run_funcotator": "true",
  20   "CNVSomaticPairWorkflow.funcotator_data_sources_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",
  21   "CNVSomaticPairWorkflow.funcotator_transcript_selection_list": "gs://broad-public-datasets/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt"
  22 }