removed all manta output files except for diploidSV.vcf

manta.wdl

@@ -90,18 +90,21 @@ task Germline {
     }
 
     output {
-        IndexedVcfFile candidateSmallIndels = object {
-            file: runDir + "/results/variants/candidateSmallIndels.vcf.gz",
-            index: runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
-        }
-        IndexedVcfFile candidateSV = object {
-            file: runDir + "/results/variants/candidateSV.vcf.gz",
-            index: runDir + "/results/variants/candidateSV.vcf.gz.tbi"
-        }
-        IndexedVcfFile diploidSV = object {
-            file: runDir + "/results/variants/diploidSV.vcf.gz",
-            index: runDir + "/results/variants/diploidSV.vcf.gz.tbi"
-        }
+
+        File mantaVCF = runDir + "/results/variants/diploidSV.vcf.gz"
+        # File mantaVCFindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
+        # IndexedVcfFile candidateSmallIndels = object {
+        #     file: runDir + "/results/variants/candidateSmallIndels.vcf.gz",
+        #     index: runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+        # }
+        # IndexedVcfFile candidateSV = object {
+        #     file: runDir + "/results/variants/candidateSV.vcf.gz",
+        #     index: runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+        # }
+        # IndexedVcfFile diploidSV = object {
+        #     file: runDir + "/results/variants/diploidSV.vcf.gz",
+        #     index: runDir + "/results/variants/diploidSV.vcf.gz.tbi"
+        # }
     }
     
     runtime {