Commit a2f2c807 authored by Sander Bollen's avatar Sander Bollen

fix more arguments

parent c91a9617
......@@ -38,6 +38,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
required("-R", r) +
required("-c", outputXcnv) +
required("-a", outputXcnvAuxFile) +
required("-p", discoverParamsFile) +
required("-s", xhmmAnalysisName)
}
......
......@@ -65,7 +65,10 @@ class XhmmMatrix(val root: Configurable) extends Xhmm {
if (inputExcludeSamples.nonEmpty && inputExcludeTargets.nonEmpty) {
repeat("--excludeTargets", inputExcludeTargets) + repeat("--excludeSamples", inputExcludeSamples)
} else if (centerData && zScoreData) {
conditional(centerData, "--centerData") + conditional(zScoreData, "--centerData") + required("--maxSdTargetRD", maxsdTargetRD)
conditional(centerData, "--centerData") +
required("--centerType", centerType) +
conditional(zScoreData, "--zScoreData") +
required("--maxSdTargetRD", maxsdTargetRD)
} else {
required("--minTargetSize", minTargetSize) +
required("--maxTargetSize", maxTargetSize) +
......
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