Commit ea2f420c authored by Sander Bollen's avatar Sander Bollen

remove superfluous side-effects

parent 129cc052
......@@ -174,20 +174,17 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
filtMatrix.outputMatrix = new File(sample.sampleDir, s"${sample.sampleId}.filtered-centered.matrix")
filtMatrix.outputExcludedSamples = Some(new File(sample.sampleDir, s"${sample.sampleId}.filtered-samples.txt"))
filtMatrix.outputExcludedTargets = Some(new File(sample.sampleDir, s"${sample.sampleId}.filtered-targets.txt"))
add(filtMatrix)
// pca generation
val pca = new XhmmPca(this)
pca.inputMatrix = filtMatrix.outputMatrix
pca.pcaFile = new File(sample.sampleDir, s"${sample.sampleId}.pca.matrix")
add(pca)
// normalization
val normalize = new XhmmNormalize(this)
normalize.inputMatrix = filtMatrix.outputMatrix
normalize.pcaFile = pca.pcaFile
normalize.normalizeOutput = new File(sample.sampleDir, s"${sample.sampleId}.normalized.matrix")
add(normalize)
// create matrix of zscores
val zMatrix = new XhmmMatrix(this)
......@@ -198,7 +195,6 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
zMatrix.outputExcludedTargets = Some(new File(sample.sampleDir, s"${sample.sampleId}.z-filtered-targets.txt"))
zMatrix.outputExcludedSamples = Some(new File(sample.sampleDir, s"${sample.sampleId}.z-filtered-samples.txt"))
zMatrix.outputMatrix = new File(sample.sampleDir, "zscores.matrix")
add(zMatrix)
// select sample from matrix
val selector = new SampleFromMatrix(this)
......
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