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vidarrtest-regression.json.in
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[
{
"arguments": {
"hrDetect.smallsVcfFile": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/HRDetect/1.0/input_data/PANX_1309_Lv_M_WG_100-PM-033_LCM4.filter.deduped.realigned.recalibrated.mutect2.filtered.vcf.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"hrDetect.smallsVcfIndex": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/HRDetect/1.0/input_data/PANX_1309_Lv_M_WG_100-PM-033_LCM4.filter.deduped.realigned.recalibrated.mutect2.filtered.vcf.gz.tbi",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"hrDetect.segFile": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/HRDetect/1.0/input_data/PANX_1309_Lv_M_WG_100-PM-033_LCM4_segments.txt",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"hrDetect.structuralVcfFile": {
"contents": {
"configuration": "/.mounts/labs/gsi/testdata/HRDetect/1.0/input_data/PANX_1309_Lv_M_WG_100-PM-033_LCM4_somatic.somatic_filtered.delly.merged.vcf.gz",
"externalIds": [
{
"id": "TEST",
"provider": "TEST"
}
]
},
"type": "EXTERNAL"
},
"hrDetect.filterSNVs.genome": "$HG38_ROOT/hg38_random.fa",
"hrDetect.reference": "hg38",
"hrDetect.filterStructural.modules":null,
"hrDetect.filterStructural.structuralQUALfilter": null,
"hrDetect.filterStructural.jobMemory": null,
"hrDetect.filterStructural.threads": null,
"hrDetect.filterStructural.timeout": null,
"hrDetect.filterINDELs.jobMemory": null,
"hrDetect.filterINDELs.threads": null,
"hrDetect.filterINDELs.timeout": null,
"hrDetect.filterSNVs.jobMemory": null,
"hrDetect.filterSNVs.threads": null,
"hrDetect.filterSNVs.timeout": null,
"hrDetect.hrdResults.modules": null,
"hrDetect.hrdResults.sigtoolrScript": null,
"hrDetect.hrdResults.SVrefSigs": null,
"hrDetect.hrdResults.SNVrefSigs":null,
"hrDetect.hrdResults.sigtoolsBootstrap": null,
"hrDetect.hrdResults.indelCutoff": null,
"hrDetect.hrdResults.threads": null,
"hrDetect.filterINDELs.genome": "$HG38_ROOT/hg38_random.fa",
"hrDetect.filterINDELs.modules": "tabix/1.9 bcftools/1.9 hg38/p12 hg38-dac-exclusion/1.0",
"hrDetect.filterSNVs.modules": "tabix/1.9 bcftools/1.9 hg38/p12 hg38-dac-exclusion/1.0",
"hrDetect.filterINDELs.difficultRegions": "--regions-file $HG38_DAC_EXCLUSION_ROOT/hg38-dac-exclusion.v2.bed",
"hrDetect.filterSNVs.difficultRegions": "--regions-file $HG38_DAC_EXCLUSION_ROOT/hg38-dac-exclusion.v2.bed",
"hrDetect.filterINDELs.VAF": 0.01,
"hrDetect.filterSNVs.VAF": 0.01,
"hrDetect.plotIt": "FALSE",
"hrDetect.filterSNVs.QUALfilter": "FILTER~'haplotype' | FILTER~'clustered_events' | FILTER~'multiallelic' | FILTER~'slippage' |FILTER~'weak_evidence' | FILTER~'strand_bias' | FILTER~'position' | FILTER~'normal_artifact' | FILTER~'map_qual' | FILTER~'germline' | FILTER~'fragment' | FILTER~'contamination' | FILTER~'base_qual'",
"hrDetect.filterINDELs.QUALfilter": "FILTER~'haplotype' | FILTER~'clustered_events' | FILTER~'multiallelic' | FILTER~'slippage' |FILTER~'weak_evidence' | FILTER~'strand_bias' | FILTER~'position' | FILTER~'normal_artifact' | FILTER~'map_qual' | FILTER~'germline' | FILTER~'fragment' | FILTER~'contamination' | FILTER~'base_qual'" ,
"hrDetect.hrdResults.timeout": 5,
"hrDetect.hrdResults.jobMemory": 30,
"hrDetect.hrdResults.tissue": "Pancreas",
"hrDetect.outputFileNamePrefix": "PANX_1309"
},
"description": "HRDetect workflow test",
"engineArguments": {
"write_to_cache": false,
"read_from_cache": false
},
"id": "PANX_1309Test",
"metadata": {
"hrDetect.hrd_signatures": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_HRDetect_PANX_1309Test_@JENKINSID@"
}
],
"type": "ALL"
},
"hrDetect.SBS_exposures": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_HRDetect_PANX_1309Test_@JENKINSID@"
}
],
"type": "ALL"
},
"hrDetect.SV_exposures": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_HRDetect_PANX_1309Test_@JENKINSID@"
}
],
"type": "ALL"
},
"hrDetect.ID_catalog": {
"contents": [
{
"outputDirectory": "@SCRATCH@/@DATE@_Workflow_HRDetect_PANX_1309Test_@JENKINSID@"
}
],
"type": "ALL"
}
},
"validators": [
{
"metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
"metrics_compare": "@CHECKOUT@/tests/compare.sh",
"output_metrics": "/.mounts/labs/gsi/testdata/HRDetect/1.0/output_metrics/PANX_1309_Test.metrics",
"type": "script"
}
]
}
]