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Have all significant XHMM commands be run with LongRunTime

This commit is contained in:
Menachem Fromer 2013-03-06 10:18:23 -05:00
parent 928f646afd
commit 5577715ae2
1 changed files with 6 additions and 6 deletions
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12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/CNV/xhmmCNVpipeline.scala
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@ -196,7 +196,7 @@ class xhmmCNVpipeline extends QScript {
} }
addAll(docs) addAll(docs)
val mergeDepths = new MergeGATKdepths(docs.map(u => u.intervalSampleOut), outputBase.getPath + RD_OUTPUT_SUFFIX, "_mean_cvg", xhmmExec, sampleIDsMap, sampleIDsMapFromColumn, sampleIDsMapToColumn, None, false) with WholeMatrixMemoryLimit val mergeDepths = new MergeGATKdepths(docs.map(u => u.intervalSampleOut), outputBase.getPath + RD_OUTPUT_SUFFIX, "_mean_cvg", xhmmExec, sampleIDsMap, sampleIDsMapFromColumn, sampleIDsMapToColumn, None, false) with WholeMatrixMemoryLimit with LongRunTime
add(mergeDepths) add(mergeDepths)
var excludeTargets : List[File] = List[File]() var excludeTargets : List[File] = List[File]()
@ -305,7 +305,7 @@ class xhmmCNVpipeline extends QScript {
} }
} }
class FilterCenterRawMatrix(inputParam: File, excludeTargetsIn : List[File]) extends CommandLineFunction with WholeMatrixMemoryLimit { class FilterCenterRawMatrix(inputParam: File, excludeTargetsIn : List[File]) extends CommandLineFunction with WholeMatrixMemoryLimit with LongRunTime {
@Input(doc = "") @Input(doc = "")
val input = inputParam val input = inputParam
@ -335,7 +335,7 @@ class xhmmCNVpipeline extends QScript {
override def description = "Filters samples and targets and then mean-centers the targets: " + command override def description = "Filters samples and targets and then mean-centers the targets: " + command
} }
class PCA(inputParam: File) extends CommandLineFunction with WholeMatrixMemoryLimit { class PCA(inputParam: File) extends CommandLineFunction with WholeMatrixMemoryLimit with LongRunTime {
@Input(doc = "") @Input(doc = "")
val input = inputParam val input = inputParam
@ -358,7 +358,7 @@ class xhmmCNVpipeline extends QScript {
override def description = "Runs PCA on mean-centered data: " + command override def description = "Runs PCA on mean-centered data: " + command
} }
class Normalize(pca: PCA) extends CommandLineFunction { class Normalize(pca: PCA) extends CommandLineFunction with LongRunTime {
@Input(doc = "") @Input(doc = "")
val input = pca.input val input = pca.input
@ -387,7 +387,7 @@ class xhmmCNVpipeline extends QScript {
override def description = "Normalizes mean-centered data using PCA information: " + command override def description = "Normalizes mean-centered data using PCA information: " + command
} }
class FilterAndZscoreNormalized(inputParam: File) extends CommandLineFunction with WholeMatrixMemoryLimit { class FilterAndZscoreNormalized(inputParam: File) extends CommandLineFunction with WholeMatrixMemoryLimit with LongRunTime {
@Input(doc = "") @Input(doc = "")
val input = inputParam val input = inputParam
@ -413,7 +413,7 @@ class xhmmCNVpipeline extends QScript {
override def description = "Filters and z-score centers (by sample) the PCA-normalized data: " + command override def description = "Filters and z-score centers (by sample) the PCA-normalized data: " + command
} }
class FilterOriginalData(inputParam: File, filt1: FilterCenterRawMatrix, filt2: FilterAndZscoreNormalized) extends CommandLineFunction with WholeMatrixMemoryLimit { class FilterOriginalData(inputParam: File, filt1: FilterCenterRawMatrix, filt2: FilterAndZscoreNormalized) extends CommandLineFunction with WholeMatrixMemoryLimit with LongRunTime {
@Input(doc = "") @Input(doc = "")
val input = inputParam val input = inputParam