Added DeepTrio wdl with workflow to call DeepTrio.

wdl/pipelines/TechAgnostic/VariantCalling/DeepTrio.wdl

@@ -0,0 +1,65 @@
+version 1.0
+
+import "../../../tasks/VariantCalling/DeepVariant.wdl" as DeepVariant
+
+workflow DeepTrio {
+    input {
+        File parent1_bam
+        File parent1_bai
+        String parent1_sample_id
+
+        File parent2_bam
+        File parent2_bai
+        String parent2_sample_id
+
+        File proband_bam
+        File proband_bai
+        String proband_sample_id
+
+        File ref_fasta
+        File ref_fasta_fai
+        File ref_fasta_dict
+
+        String model_type = "WGS"
+    }
+
+    call DeepVariant.DeepTrio as t_001_DeepTrio {
+        input:
+            parent1_bam = parent1_bam,
+            parent1_bai = parent1_bai,
+            parent1_sample_id = parent1_sample_id,
+
+            parent2_bam = parent2_bam,
+            parent2_bai = parent2_bai,
+            parent2_sample_id = parent2_sample_id,
+
+            proband_bam = proband_bam,
+            proband_bai = proband_bai,
+            proband_sample_id = proband_sample_id,
+
+            ref_fasta = ref_fasta,
+            ref_fasta_fai = ref_fasta_fai,
+            ref_fasta_dict = ref_fasta_dict,
+
+            model_type = model_type,
+    }
+
+    output {
+        File parent1_vcf = t_001_DeepTrio.parent1_vcf
+        File parent1_vcf_index = t_001_DeepTrio.parent1_vcf_index
+        File parent1_gvcf = t_001_DeepTrio.parent1_gvcf
+        File parent1_gvcf_index = t_001_DeepTrio.parent1_gvcf_index
+
+        File parent2_vcf = t_001_DeepTrio.parent2_vcf
+        File parent2_vcf_index = t_001_DeepTrio.parent2_vcf_index
+        File parent2_gvcf = t_001_DeepTrio.parent2_gvcf
+        File parent2_gvcf_index = t_001_DeepTrio.parent2_gvcf_index
+
+        File proband_vcf = t_001_DeepTrio.proband_vcf
+        File proband_vcf_index = t_001_DeepTrio.proband_vcf_index
+        File proband_gvcf = t_001_DeepTrio.proband_gvcf
+        File proband_gvcf_index = t_001_DeepTrio.proband_gvcf_index
+
+        File logs = t_001_DeepTrio.logs
+    }
+}