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Commit dc1f66b5 authored by cagaser's avatar cagaser
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samtools.wdl: add include header option to samtools view

parent 8ef3d860
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......@@ -209,6 +209,7 @@ task View {
File inFile
File? referenceFasta
String outputFileName
Boolean? includeHeader
Boolean? outputBam
Boolean? uncompressedBamOutput
Int? includeFilter
......@@ -225,6 +226,7 @@ task View {
samtools view \
~{"-T " + referenceFasta} \
~{"-o " + outputFileName} \
~{true="-h " false="" includeHeader} \
~{true="-b " false="" outputBam} \
~{true="-u " false="" uncompressedBamOutput} \
~{"-f " + includeFilter} \
......
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