diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
index ceed849ff8a1a09554b861bdb0f12808440ec66c..8ecc014340471ac29383e4bf8ea050145541c672 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.core.annotations
import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
+import nl.lumc.sasc.biopet.utils.LazyCheck
import org.broadinstitute.gatk.queue.QScript
/**
@@ -27,21 +28,21 @@ trait AnnotationBed extends BiopetQScript { qscript: QScript =>
trait AnnotationRefFlat extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
- lazy val annotationRefFlat: File = {
+ lazy val annotationRefFlat = new LazyCheck({
val file: File = config("annotation_refflat", freeVar = true)
inputFiles :+ InputFile(file, config("annotation_refflat_md5", freeVar = true))
file
- }
+ })
}
trait RibosomalRefFlat extends BiopetQScript { qscript: QScript =>
/** GTF reference file */
- lazy val ribosomalRefFlat: Option[File] = {
+ lazy val ribosomalRefFlat = new LazyCheck({
val file: Option[File] = config("ribosome_refflat", freeVar = true)
file match {
case Some(f) => inputFiles :+ InputFile(f, config("ribosome_refflat_md5", freeVar = true))
- case _ =>
+ case _ =>
}
file
- }
+ })
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala
new file mode 100644
index 0000000000000000000000000000000000000000..4fdb70712175e9501cead1b54068120afa7787bd
--- /dev/null
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/LazyCheck.scala
@@ -0,0 +1,16 @@
+package nl.lumc.sasc.biopet.utils
+
+/**
+ * Created by pjvan_thof on 1/25/16.
+ */
+class LazyCheck[T](function: => T) {
+ private var _isSet = false
+ def isSet = _isSet
+ lazy val value = {
+ val chache = function
+ _isSet = true
+ chache
+ }
+ def apply() = value
+ def get = value
+}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 6b4f93b4d9dad3f59e97145ed05d41b835c4442c..0e7088e6ea660cd2287f496ecee3695113972535 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ StrandProtocol, ExpMeasur
import nl.lumc.sasc.biopet.pipelines.gentrap.measures._
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
-import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.{ LazyCheck, Logging }
import nl.lumc.sasc.biopet.utils.config._
import org.broadinstitute.gatk.queue.QScript
import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
@@ -53,15 +53,17 @@ class Gentrap(val root: Configurable) extends QScript
/** Expression measurement modes */
// see the enumeration below for valid modes
- lazy val expMeasures = config("expression_measures", default = Nil).asStringList.map(value =>
- ExpMeasures.values.find(_.toString == Gentrap.camelize(value)) match {
- case Some(v) => v
- case _ => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
- }
- ).toSet
+ lazy val expMeasures = new LazyCheck({
+ config("expression_measures", default = Nil).asStringList.map(value =>
+ ExpMeasures.values.find(_.toString == Gentrap.camelize(value)) match {
+ case Some(v) => v
+ case _ => throw new IllegalArgumentException(s"'$value' is not a valid Expression measurement")
+ }
+ ).toSet
+ })
/** Strandedness modes */
- val strandProtocol: StrandProtocol.Value = {
+ lazy val strandProtocol = new LazyCheck({
val value: String = config("strand_protocol")
StrandProtocol.values.find(_.toString == Gentrap.camelize(value)) match {
case Some(v) => v
@@ -69,23 +71,25 @@ class Gentrap(val root: Configurable) extends QScript
Logging.addError(s"'$other' is no strand_protocol or strand_protocol is not given")
StrandProtocol.NonSpecific
}
- }
+ })
/** Whether to remove rRNA regions or not */
lazy val removeRibosomalReads: Boolean = config("remove_ribosomal_reads", default = false)
/** Default pipeline config */
override def defaults = Map(
- "htseqcount" -> Map("stranded" -> (strandProtocol match {
+ "htseqcount" -> (if (strandProtocol.isSet) Map("stranded" -> (strandProtocol() match {
case StrandProtocol.NonSpecific => "no"
case StrandProtocol.Dutp => "reverse"
case otherwise => throw new IllegalStateException(otherwise.toString)
- })),
- "cufflinks" -> Map("library_type" -> (strandProtocol match {
+ }))
+ else Map()),
+ "cufflinks" -> (if (strandProtocol.isSet) Map("library_type" -> (strandProtocol() match {
case StrandProtocol.NonSpecific => "fr-unstranded"
case StrandProtocol.Dutp => "fr-firststrand"
case otherwise => throw new IllegalStateException(otherwise.toString)
- })),
+ }))
+ else Map()),
"merge_strategy" -> "preprocessmergesam",
"gsnap" -> Map(
"novelsplicing" -> 1,
@@ -95,14 +99,14 @@ class Gentrap(val root: Configurable) extends QScript
"shivavariantcalling" -> Map("variantcallers" -> List("varscan_cns_singlesample")),
"bammetrics" -> Map(
"transcript_refflat" -> annotationRefFlat,
- "collectrnaseqmetrics" -> ((if (strandProtocol != null) Map(
- "strand_specificity" -> (strandProtocol match {
+ "collectrnaseqmetrics" -> ((if (strandProtocol.isSet) Map(
+ "strand_specificity" -> (strandProtocol() match {
case StrandProtocol.NonSpecific => StrandSpecificity.NONE.toString
case StrandProtocol.Dutp => StrandSpecificity.SECOND_READ_TRANSCRIPTION_STRAND.toString
case otherwise => throw new IllegalStateException(otherwise.toString)
})
)
- else Map()) ++ (if (ribosomalRefFlat != null) ribosomalRefFlat.map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))
+ else Map()) ++ (if (ribosomalRefFlat.isSet) ribosomalRefFlat().map("ribosomal_intervals" -> _.getAbsolutePath).toList else Nil))
),
"cutadapt" -> Map("minimum_length" -> 20),
// avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
@@ -115,22 +119,22 @@ class Gentrap(val root: Configurable) extends QScript
)
)
- lazy val fragmentsPerGene = if (expMeasures.contains(ExpMeasures.FragmentsPerGene))
+ lazy val fragmentsPerGene = if (expMeasures().contains(ExpMeasures.FragmentsPerGene))
Some(new FragmentsPerGene(this)) else None
- lazy val fragmentsPerExon = if (expMeasures.contains(ExpMeasures.FragmentsPerExon))
+ lazy val fragmentsPerExon = if (expMeasures().contains(ExpMeasures.FragmentsPerExon))
Some(new FragmentsPerExon(this)) else None
- lazy val baseCounts = if (expMeasures.contains(ExpMeasures.BaseCounts))
+ lazy val baseCounts = if (expMeasures().contains(ExpMeasures.BaseCounts))
Some(new BaseCounts(this)) else None
- lazy val cufflinksBlind = if (expMeasures.contains(ExpMeasures.CufflinksBlind))
+ lazy val cufflinksBlind = if (expMeasures().contains(ExpMeasures.CufflinksBlind))
Some(new CufflinksBlind(this)) else None
- lazy val cufflinksGuided = if (expMeasures.contains(ExpMeasures.CufflinksGuided))
+ lazy val cufflinksGuided = if (expMeasures().contains(ExpMeasures.CufflinksGuided))
Some(new CufflinksGuided(this)) else None
- lazy val cufflinksStrict = if (expMeasures.contains(ExpMeasures.CufflinksStrict))
+ lazy val cufflinksStrict = if (expMeasures().contains(ExpMeasures.CufflinksStrict))
Some(new CufflinksStrict(this)) else None
def executedMeasures = (fragmentsPerGene :: fragmentsPerExon :: baseCounts :: cufflinksBlind ::
@@ -148,14 +152,14 @@ class Gentrap(val root: Configurable) extends QScript
/** Files that will be listed in the summary file */
override def summaryFiles: Map[String, File] = super.summaryFiles ++ Map(
- "annotation_refflat" -> annotationRefFlat
+ "annotation_refflat" -> annotationRefFlat()
) ++ Map(
- "ribosome_refflat" -> ribosomalRefFlat
+ "ribosome_refflat" -> ribosomalRefFlat()
).collect { case (key, Some(value)) => key -> value }
/** Pipeline settings shown in the summary file */
override def summarySettings: Map[String, Any] = super.summarySettings ++ Map(
- "expression_measures" -> expMeasures.toList.map(_.toString),
+ "expression_measures" -> expMeasures().toList.map(_.toString),
"strand_protocol" -> strandProtocol.toString,
"call_variants" -> shivaVariantcalling.isDefined,
"remove_ribosomal_reads" -> removeRibosomalReads
@@ -165,7 +169,7 @@ class Gentrap(val root: Configurable) extends QScript
override def init(): Unit = {
super.init()
- if (expMeasures.isEmpty) Logging.addError("'expression_measures' is missing in the config")
+ if (expMeasures().isEmpty) Logging.addError("'expression_measures' is missing in the config")
executedMeasures.foreach(x => x.outputDir = new File(outputDir, "expresion_measures" + File.separator + x.name))
}
@@ -197,7 +201,7 @@ class Gentrap(val root: Configurable) extends QScript
override lazy val preProcessBam = if (removeRibosomalReads) {
val job = new WipeReads(qscript)
job.inputBam = bamFile.get
- ribosomalRefFlat.foreach(job.intervalFile = _)
+ ribosomalRefFlat().foreach(job.intervalFile = _)
job.outputBam = createFile(".cleaned.bam")
job.discardedBam = createFile(".rrna.bam")
add(job)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
index 25ed2719b22088d8469922e6c50a91746ea80bfe..3ad9146b62648aa438f407f4c6e47b0bcaf00f73 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
@@ -21,7 +21,7 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
baseCounter.bamFile = file
baseCounter.outputDir = new File(outputDir, id)
baseCounter.prefix = id
- baseCounter.refFlat = annotationRefFlat
+ baseCounter.refFlat = annotationRefFlat()
add(baseCounter)
id -> baseCounter
}