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Commit ed6d2cf2 authored by António Paulo's avatar António Paulo
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fix command according to style guideline 

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gatk.wdl
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...@@ -446,7 +446,7 @@ task FilterMutectCalls { ...@@ -446,7 +446,7 @@ task FilterMutectCalls {
FilterMutectCalls \ FilterMutectCalls \
-R ~{referenceFasta} \ -R ~{referenceFasta} \
-V ~{unfilteredVcf} \ -V ~{unfilteredVcf} \
-O ${outputVcf} \ -O ~{outputVcf} \
~{"--contamination-table " + contaminationTable} \ ~{"--contamination-table " + contaminationTable} \
~{"--tumor-segmentation " + mafTumorSegments} \ ~{"--tumor-segmentation " + mafTumorSegments} \
~{"--ob-priors " + artifactPriors} \ ~{"--ob-priors " + artifactPriors} \
...@@ -508,7 +508,7 @@ task SplitNCigarReads { ...@@ -508,7 +508,7 @@ task SplitNCigarReads {
task CombineVariants { task CombineVariants {
input { input {
String installDir = "/usr" String installDir = "/usr" # .jar location in the docker image
File referenceFasta File referenceFasta
File referenceFastaFai File referenceFastaFai
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