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inputs.gcp.json
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inputs.gcp.json
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{
"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": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai"
},
"pbsv_splits": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json",
"tandem_repeat_bed": "gs://pacbio-wdl/dataset/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed",
"trgt_tandem_repeat_bed": "gs://pacbio-wdl/dataset/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed",
"hificnv_exclude_bed": {
"data": "gs://pacbio-wdl/dataset/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi"
},
"hificnv_expected_bed_male": "gs://pacbio-wdl/dataset/GRCh38/hificnv/expected_cn.hg38.XY.bed",
"hificnv_expected_bed_female": "gs://pacbio-wdl/dataset/GRCh38/hificnv/expected_cn.hg38.XX.bed",
"gnomad_af": "gs://pacbio-wdl/dataset/GRCh38/slivar_gnotate/gnomad.hg38.v3.custom.v1.zip",
"hprc_af": "gs://pacbio-wdl/dataset/GRCh38/slivar_gnotate/hprc.deepvariant.glnexus.hg38.v1.zip",
"gff": "gs://pacbio-wdl/dataset/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz",
"population_vcfs": [
{
"data": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/EEE_SV-Pop_1.ALL.sites.20181204.vcf.gz.tbi"
},
{
"data": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/nstd166.GRCh38.variant_call.vcf.gz",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/nstd166.GRCh38.variant_call.vcf.gz.tbi"
},
{
"data": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/hprc.GRCh38.pbsv.vcf.gz",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/hprc.GRCh38.pbsv.vcf.gz.tbi"
},
{
"data": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/ont_sv_high_confidence_SVs.sorted.vcf.gz",
"data_index": "gs://pacbio-wdl/dataset/GRCh38/sv_pop_vcfs/ont_sv_high_confidence_SVs.sorted.vcf.gz.tbi"
}
]
},
"humanwgs.slivar_data": {
"slivar_js": "gs://pacbio-wdl/dataset/slivar/slivar-functions.v0.2.8.js",
"hpo_terms": "gs://pacbio-wdl/dataset/hpo/hpoTerms.txt",
"hpo_dag": "gs://pacbio-wdl/dataset/hpo/hpoDag.txt",
"hpo_annotations": "gs://pacbio-wdl/dataset/hpo/ensembl.hpoPhenotype.tsv",
"ensembl_to_hgnc": "gs://pacbio-wdl/dataset/genes/ensembl.hgncSymbol.tsv",
"lof_lookup": "gs://pacbio-wdl/dataset/slivar/lof_lookup.v2.1.1.txt",
"clinvar_lookup": "gs://pacbio-wdl/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": "GCP",
"humanwgs.zones": "String",
"humanwgs.preemptible": "Boolean"
}