Merge pull request #16 from broadinstitute/BenchmarkCNV

BenchmarkCNV wdl

.dockstore.yml

@@ -17,11 +17,6 @@ workflows:
    primaryDescriptorPath: /CollectSamError/CollectSamErrorMetrics.wdl
    testParameterFiles:
    - /CollectSamError/CollectSamErrorMetrics.inputs.json
- - name: BenchmarkCNV
-   subclass: WDL
-   primaryDescriptorPath: /BenchmarkCNV/BenchmarkCNV.wdl
-   testParameterFiles:
-   - /BenchmarkCNV/BenchmarkCNV_test.json
  - name: GATK4_CNV
    subclass: WDL
    primaryDescriptorPath: /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNV.wdl
@@ -79,8 +74,24 @@ workflows:
    primaryDescriptorPath: /checkBaitSetName/checkBaitSetName.wdl
    testParameterFiles:
     - /checkBaitSetName/checkBaitSetName.inputs.json
+ - name: SelectSampleFromCallSet
+   subclass: WDL
+   primaryDescriptorPath: /BenchmarkCNV/SelectSampleFromCallSet/SelectSampleFromCallSet.wdl
+   testParameterFiles:
+   - /BenchmarkCNV/SelectSampleFromCallSet/SelectSampleFromCallSet.inputs.json
+ - name: MergeVCF
+   subclass: WDL
+   primaryDescriptorPath: /BenchmarkCNV/MergeVCF/MergeVCF.wdl
+   testParameterFiles:
+   - /BenchmarkCNV/MergeVCF/MergeVCF.inputs.json
+ - name: BenchmarkCNV
+   subclass: WDL
+   primaryDescriptorPath: /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.wdl
+   testParameterFiles:
+   - /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.inputs.json
  - name: checkBaitSetName_dev
    subclass: WDL
    primaryDescriptorPath: /checkBaitSetName/checkBaitSetName.dev.wdl
    testParameterFiles:
     - /checkBaitSetName/checkBaitSetName.dev.inputs.json
+

BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.inputs.json

@@ -0,0 +1,15 @@
+{
+  "Benchmark_CNV_Caller.bedfile": "gs://gptag/tag_1455_Dragen_CNV_Caller_Validation/HighConfidenceRegion_BedFile/HG002_hg38_SVs_Tier1_v0.6.bed",
+  "Benchmark_CNV_Caller.BenchmarkCNV.mem_size": 4,
+  "Benchmark_CNV_Caller.wittyer_docker": "us.gcr.io/tag-team-160914/wittyer:v2",
+  "Benchmark_CNV_Caller.BenchmarkCNV.mem": 4,
+  "Benchmark_CNV_Caller.wittyer_evaluation_mode": "CrossTypeAndSimpleCounting",
+  "Benchmark_CNV_Caller.BenchmarkCNV.disk_size": 100,
+  "Benchmark_CNV_Caller.wittyer4mat_docker": "us.gcr.io/tag-team-160914/wittyer4mat:v11-outstat-broom",
+  "Benchmark_CNV_Caller.eval_vcf": "gs://dragen_v_3_10_4_cnv_validation/hg38_ml/NA24385_hg38/NA24385.cnv.vcf.gz",
+  "Benchmark_CNV_Caller.BenchmarkCNV.disk_space": 100,
+  "Benchmark_CNV_Caller.truth_sample_name": "NA24385",
+  "Benchmark_CNV_Caller.truth_vcf": "gs://fc-cd2e8270-8c64-4f10-bcfb-2f1b5f44aee4/submissions/47e84385-8207-4ad0-a412-b2c113efb470/SelectSampleFromCallSet/17210bc4-e6c8-4ce5-bb23-486fcb18ab89/call-SelectSample/NA24385_filtered.vcf",
+  "Benchmark_CNV_Caller.query_sample_name": "SM-MVWA8",
+  "Benchmark_CNV_Caller.wittyer_config": "gs://gptag/tag_1455_Dragen_CNV_Caller_Validation/wittyerConfigFile/cnv-config.json"
+}