M2 cnv updates 1534

GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json

@@ -4,6 +4,7 @@
   "CNVSomaticPairWorkflow.mem_gb_for_call_copy_ratio_segments": "Int? (optional)",
   "CNVSomaticPairWorkflow.num_smoothing_iterations_per_fit": "Int? (optional)",
   "CNVSomaticPairWorkflow.ModelSegmentsNormal.output_dir": "String? (optional)",
+  "CNVSomaticPairWorkflow.is_run_contam": "Boolean? (optional)",
   "CNVSomaticPairWorkflow.mem_gb_for_funcotator": "Int? (optional)",
   "CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.output_dir": "String? (optional)",
   "CNVSomaticPairWorkflow.calling_copy_ratio_z_score_threshold": "Float? (optional)",
@@ -29,13 +30,15 @@
   "CNVSomaticPairWorkflow.funcotator_cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.funcotator_is_removing_untared_datasources": "Boolean? (optional)",
   "CNVSomaticPairWorkflow.emergency_extra_disk": "Int? (optional)",
+  "CNVSomaticPairWorkflow.CalculateContamination.additional_disk": "Int? (optional)",
   "CNVSomaticPairWorkflow.ModelSegmentsNormal.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.CallCopyRatioSegmentsTumor.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.ModelSegmentsNormal.normal_allelic_counts": "File? (optional)",
   "CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.output_dir": "String? (optional)",
   "CNVSomaticPairWorkflow.funcotator_excluded_fields": "Array[String]? (optional)",
   "CNVSomaticPairWorkflow.point_size_copy_ratio": "Float? (optional)",
   "CNVSomaticPairWorkflow.ref_fasta_fai": "File",
+  "CNVSomaticPairWorkflow.CalculateContamination.contamination_vcf_index": "File",
   "CNVSomaticPairWorkflow.CollectCountsTumor.cpu": "Int? (optional)",
   "CNVSomaticPairWorkflow.kernel_approximation_dimension": "Int? (optional)",
   "CNVSomaticPairWorkflow.outlier_neutral_segment_copy_ratio_z_score_threshold": "Float? (optional)",
@@ -114,6 +117,7 @@
   "CNVSomaticPairWorkflow.boot_disk_space_gb_for_oncotator": "Int? (optional)",
   "CNVSomaticPairWorkflow.bin_length": "Int? (optional)",
   "CNVSomaticPairWorkflow.additional_args_for_funcotator": "String? (optional)",
+  "CNVSomaticPairWorkflow.CalculateContamination.contamination_vcf": "File",
   "CNVSomaticPairWorkflow.kernel_variance_allele_fraction": "Float? (optional)"
 }
 

GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.wdl

@@ -40,6 +40,7 @@ version 1.0
 import "https://raw.githubusercontent.com/broadinstitute/gatk/4.2.0.0/scripts/cnv_wdl/cnv_common_tasks.wdl" as CNVTasks
 import "https://raw.githubusercontent.com/broadinstitute/gatk/4.2.0.0/scripts/cnv_wdl/somatic/cnv_somatic_oncotator_workflow.wdl" as CNVOncotator
 import "https://raw.githubusercontent.com/broadinstitute/gatk/4.2.0.0/scripts/cnv_wdl/somatic/cnv_somatic_funcotate_seg_workflow.wdl" as CNVFuncotateSegments
+import "https://api.firecloud.org/ga4gh/v1/tools/GP-TAG:CalculateContamination/versions/13/plain-WDL/descriptor" as CalculateContamination
 
 workflow CNVSomaticPairWorkflow {
 
@@ -67,6 +68,8 @@ workflow CNVSomaticPairWorkflow {
       Boolean? is_run_oncotator
        # For running funcotator
       Boolean? is_run_funcotator
+       # For running CalculateContamination
+      Boolean? is_run_contam
 
       File? gatk4_jar_override
       Int? preemptible_attempts
@@ -511,6 +514,19 @@ workflow CNVSomaticPairWorkflow {
                  cpu = funcotator_cpu
         }
     }
+    if (select_first([is_run_contam, false])) {
+        call CalculateContamination.CheckContamination as CalculateContamination {
+            input: tumor_cram_or_bam = tumor_bam,
+                   tumor_crai_or_bai = tumor_bam_idx,
+                   normal_cram_or_bam = normal_bam,
+                   normal_crai_or_bai = normal_bam_idx,
+                   reference = ref_fasta,
+                   reference_index = ref_fasta_fai,
+                   reference_dict = ref_fasta_dict,
+                   gatk_docker = gatk_docker,
+                   gatk_override = gatk4_jar_override
+        }
+    }
 
     output {
         File preprocessed_intervals = PreprocessIntervals.preprocessed_intervals
@@ -579,6 +595,12 @@ workflow CNVSomaticPairWorkflow {
         File oncotated_called_gene_list_file_tumor = select_first([CNVOncotatorWorkflow.oncotated_called_gene_list_file, "null"])
         File funcotated_called_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_seg_simple_tsv, "null"])
         File funcotated_called_gene_list_file_tumor = select_first([CNVFuncotateSegmentsWorkflow.funcotated_gene_list_tsv, "null"])
+
+        File? pileups = CalculateContamination.pileups
+        File? normal_pileups = CalculateContamination.normal_pileups
+        File? contamination_table = CalculateContamination.contamination_table
+        File? maf_segments = CalculateContamination.maf_segments
+        Float? contamination = CalculateContamination.contamination
     }
 }
 
@@ -906,4 +928,4 @@ task PlotModeledSegments {
     output {
         File modeled_segments_plot = "~{output_dir_}/~{entity_id}.modeled.png"
     }
-}
+}

GATK_CNV_Mutect2/GATK4_CNV/README.md

@@ -1,8 +1,7 @@
 # GATK_CNV
 Workflow for calling somatic copy number variants as tumor-normal or tumor-only mode. Supports both WGS and WES.
 
-This WDL is originally from [CNV_Somatic_Panel_Workflow](https://github.com/gatk-workflows/gatk4-somatic-cnvs) and 
+This WDL is originally from [CNV_Somatic_Pair_Workflow](https://dockstore.org/workflows/github.com/broadinstitute/gatk/cnv_somatic_pair_workflow:4.2.0.0?tab=files) and 
 is modified to output the number of segments, amplifications, and deletions in a Terra workspace table.
 
 
-**UNDER CONSTRUCTION**