inputs.azure.json

{
  "humanwgs.cohort": {
    "cohort_id": "String",
    "samples": [
      {
        "sample_id": "String",
        "movie_bams": [
          "File"
        ],
        "sex": "String?",
        "affected": "Boolean",
        "father_id": "String?",
        "mother_id": "String?"
      }
    ],
    "phenotypes": [
      "String"
    ]
  },
  "humanwgs.reference": {
    "name": "GRCh38",
    "fasta": {
      "data": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
      "data_index": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
    },
    "pbsv_splits": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
    "tandem_repeat_bed": "/datasetpbrarediseases/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
    "trgt_tandem_repeat_bed": "/datasetpbrarediseases/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
    "hificnv_exclude_bed": {
      "data": "/datasetpbrarediseases/dataset/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz",
      "data_index": "/datasetpbrarediseases/dataset/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi"
    },
    "hificnv_expected_bed_male": "/datasetpbrarediseases/dataset/GRCh38/hificnv/expected_cn.hg38.XY.bed",
    "hificnv_expected_bed_female": "/datasetpbrarediseases/dataset/GRCh38/hificnv/expected_cn.hg38.XX.bed",
    "gnomad_af": "/datasetpbrarediseases/dataset/GRCh38/slivar_gnotate/gnomad.hg38.v3.custom.v1.zip",
    "hprc_af": "/datasetpbrarediseases/dataset/GRCh38/slivar_gnotate/hprc.deepvariant.glnexus.hg38.v1.zip",
    "gff": "/datasetpbrarediseases/dataset/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz",
    "population_vcfs": [
      {
          "data": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz",
          "data_index": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz.tbi"
      },
      {
          "data": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/nstd166.GRCh38.variant_call.vcf.gz",
          "data_index": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/nstd166.GRCh38.variant_call.vcf.gz.tbi"
      },
      {
          "data": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/hprc.GRCh38.pbsv.vcf.gz",
          "data_index": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/hprc.GRCh38.pbsv.vcf.gz.tbi"
      },
      {
          "data": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/ont_sv_high_confidence_SVs.sorted.vcf.gz",
          "data_index": "/datasetpbrarediseases/dataset/GRCh38/sv_pop_vcfs/ont_sv_high_confidence_SVs.sorted.vcf.gz.tbi"
      }
    ]
  },
  "humanwgs.slivar_data": {
    "slivar_js": "/datasetpbrarediseases/dataset/slivar/slivar-functions.v0.2.8.js",
    "hpo_terms": "/datasetpbrarediseases/dataset/hpo/hpoTerms.txt",
    "hpo_dag": "/datasetpbrarediseases/dataset/hpo/hpoDag.txt",
    "hpo_annotations": "/datasetpbrarediseases/dataset/hpo/ensembl.hpoPhenotype.tsv",
    "ensembl_to_hgnc": "/datasetpbrarediseases/dataset/genes/ensembl.hgncSymbol.tsv",
    "lof_lookup": "/datasetpbrarediseases/dataset/slivar/lof_lookup.v2.1.1.txt",
    "clinvar_lookup": "/datasetpbrarediseases/dataset/slivar/clinvar_gene_desc.20221214T183140.txt"
  },
  "humanwgs.deepvariant_version": "String (optional)",
  "humanwgs.deepvariant_model": "WomCompositeType {\n model -> WomCompositeType {\n data -> File\ndata_index -> File \n}\nmetadata -> File \n}? (optional)",
  "humanwgs.pbsv_call_mem_gb": "Int (optional, default = if N<=3: 64 else 96)",
  "humanwgs.glnexus_mem_gb": "Int (optional, default = 30)",
  "humanwgs.run_tertiary_analysis": "Boolean (optional, default = false)",
  "humanwgs.backend": "Azure",
  "humanwgs.preemptible": "Boolean"
}