etc/gatk-wdl/mutect2.bgi.inputs.json

   1 {
   2   "##_COMMENT1": "Runtime",
   3   "##Mutect2.oncotator_docker": "(optional) String?",
   4   "Mutect2.gatk_docker": "broadinstitute/gatk:4.0.8.1",
   5
   6   "##_COMMENT2": "Workflow options",
   7   "Mutect2.intervals": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/wgs_metrics_intervals.interval_list",
   8   "Mutect2.scatter_count": 50,
   9   "Mutect2.artifact_modes": ["G/T", "C/T"],
  10   "##_Mutect2.m2_extra_args": "(optional) String?",
  11   "##_Mutect2.m2_extra_filtering_args": "(optional) String?",
  12   "Mutect2.run_orientation_bias_filter": "False",
  13   "Mutect2.run_oncotator": "False",
  14
  15   "##_COMMENT3": "Primary inputs",
  16   "Mutect2.ref_fasta": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
  17   "Mutect2.ref_dict": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
  18   "Mutect2.ref_fai": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  19   "Mutect2.normal_bam": "/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-Normal.hg38.bam",
  20   "Mutect2.normal_bai": "/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-Normal.hg38.bai",
  21   "Mutect2.tumor_bam": "/share/FGI2017B/users/huxs/nsfcG/wgs/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/4afceaf9-6544-471c-8b94-31b88b67cc23/call-GatherBamFiles/execution/WGS-D3B.hg38.bam",
  22   "Mutect2.tumor_bai": "/share/FGI2017B/users/huxs/nsfcG/wgs/cromwell-executions/PreProcessingForVariantDiscovery_GATK4/4afceaf9-6544-471c-8b94-31b88b67cc23/call-GatherBamFiles/execution/WGS-D3B.hg38.bai",
  23
  24   "##_COMMENT4": "Primary resources",
  25   "Mutect2.pon": "/hwfssz1/pub/database/storage.googleapis.com/gatk-test-data/mutect2/M2PoN_4.0_WGS_for_public.vcf",
  26   "Mutect2.pon_index": "/hwfssz1/pub/database/storage.googleapis.com/gatk-test-data/mutect2/M2PoN_4.0_WGS_for_public.vcf.idx",
  27   "Mutect2.gnomad": "/hwfssz1/pub/database/storage.googleapis.com/gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz",
  28   "Mutect2.gnomad_index": "/hwfssz1/pub/database/storage.googleapis.com/gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz.tbi",
  29   "Mutect2.variants_for_contamination": "/hwfssz1/pub/database/storage.googleapis.com/gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz",
  30   "Mutect2.variants_for_contamination_index": "/hwfssz1/pub/database/storage.googleapis.com/gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz.tbi",
  31   "Mutect2.realignment_index_bundle": "/share/FGI2017B/pub/Ref/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.img",
  32
  33   "##_COMMENT5": "Secondary resources",
  34   "##_Mutect2.onco_ds_tar_gz": "gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz",
  35   "##_Mutect2.default_config_file": "gs://gatk-best-practices/somatic-b37/onco_config.txt",
  36   "##_Mutect2.sequencing_center": "(optional) String?",
  37   "##_Mutect2.sequence_source": "(optional) String?",
  38
  39   "##_COMMENT6": "Secondary resources",
  40   "##_Mutect2.MergeBamOuts.mem": "(optional) Int?",
  41   "##_Mutect2.SplitIntervals.mem": "(optional) Int?",
  42   "##_Mutect2.M2.mem": "(optional) Int?",
  43   "##_Mutect2.MergeVCFs.mem": "(optional) Int?",
  44   "##_Mutect2.oncotate_m2.mem": "(optional) Int?",
  45
  46   "##_COMMENT7": "Secondary resources",
  47   "##_Mutect2.onco_ds_local_db_dir": "(optional) String?",
  48   "##_Mutect2.sequencing_center": "(optional) String?",
  49   "##_Mutect2.oncotate_m2.oncotator_exe": "(optional) String?",
  50   "##_Mutect2.gatk4_override": "(optional) File?",
  51   "##_Mutect2.CollectSequencingArtifactMetrics.mem": "(optional) Int?",
  52
  53   "Mutect2.run_funcotator": "true",
  54   "Mutect2.funco_reference_version": "hg38",
  55   "Mutect2.funco_data_sources_tar_gz": "/hwfssz1/pub/database/ftp.broadinstitute.org/gsapubftp-anonymous/bundle/funcotator/funcotator_dataSources.v1.4.20180615.tar.gz",
  56   "##_Mutect2.funco_annotation_defaults": "",
  57   "##_Mutect2.funco_annotation_overrides": "",
  58   "##_Mutect2.funco_transcript_selection_list": "",
  59   "##_Mutect2.funco_transcript_selection_mode": "",
  60
  61   "##_COMMENT8": "Disk space",
  62   "##_Mutect2.MergeVCFs.disk_space_gb": "(optional) Int?",
  63   "##_Mutect2.Filter.disk_space_gb": "(optional) Int?",
  64   "##_Mutect2.M2.disk_space_gb": "(optional) Int?",
  65   "##_Mutect2.M2.disk_space_gb": 100,
  66   "##_Mutect2.oncotate_m2.disk_space_gb": "(optional) Int?",
  67   "##_Mutect2.SplitIntervals.disk_space_gb": "(optional) Int?",
  68   "##_Mutect2.MergeBamOuts.disk_space_gb": "(optional) Int?",
  69   "##_Mutect2.CollectSequencingArtifactMetrics.disk_space_gb": "(optional) Int?",
  70   "##_Mutect2.emergency_extra_disk": "(optional) Int?",
  71
  72   "##_COMMENT9": "Preemptibles",
  73   "##_Mutect2.MergeBamOuts.preemptible_attempts": "(optional) Int?",
  74   "Mutect2.preemptible_attempts": 3
  75 }