From caf64816847281f8e7e4b828678648bba34364e0 Mon Sep 17 00:00:00 2001 From: Ruben Vorderman Date: Fri, 30 Aug 2024 16:43:09 +0200 Subject: [PATCH] Also record normalized baseline calls --- clinical-validation.wdl | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/clinical-validation.wdl b/clinical-validation.wdl index eb11b2e..fb15816 100644 --- 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