Also record normalized baseline calls

biowdl · Aug 30, 2024 · caf6481 · caf6481
1 parent 6e49003
commit caf6481
Showing 1 changed file with 9 additions and 7 deletions.
diff --git a/clinical-validation.wdl b/clinical-validation.wdl
@@ -208,19 +208,21 @@ workflow ClinicalValidation {
     output {
         Array[File] indelStats = flatten(evalIndels.allStats)
         Array[File] SNPStats = flatten(evalSNPs.allStats)
-        Array[File] indelVcf = selectIndelsCall.outputVcf
-        Array[File] indelVcfIndex = selectIndelsCall.outputVcfIndex
-        Array[File] SNPVcf = selectSNPsCall.outputVcf
-        Array[File] SNPVcfIndex = selectSNPsCall.outputVcfIndex
-
-        Array[File] normalizedVcf = indexNormalizedCall.compressed
-        Array[File] normalizedVcfIndex = indexNormalizedCall.index
 
+        Array[File] normalizedBaselineVcf = indexBaselineVcf.compressed
+        Array[File] normalizedBaselineVcfIndex = indexBaselineVcf.index
         Array[File] BaselineIndelVcf = selectIndelsBaseline.outputVcf
         Array[File] BaselineIndelVcfIndex = selectIndelsBaseline.outputVcfIndex
         Array[File] BaselineSNPVcf = selectSNPsBaseline.outputVcf
         Array[File] BaselineSNPVcfIndex = selectSNPsBaseline.outputVcfIndex
 
+        Array[File] normalizedVcf = indexNormalizedCall.compressed
+        Array[File] normalizedVcfIndex = indexNormalizedCall.index
+        Array[File] indelVcf = selectIndelsCall.outputVcf
+        Array[File] indelVcfIndex = selectIndelsCall.outputVcfIndex
+        Array[File] SNPVcf = selectSNPsCall.outputVcf
+        Array[File] SNPVcfIndex = selectSNPsCall.outputVcfIndex
+
         File? indelTSV = parseSummary.IndelTSV
         File? snpTSV = parseSummary.SnpTSV
         File? htmlGraph = parseSummary.HtmlGraph