Commit 4ff7fc14 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing library tags for variantcalling

(cherry picked from commit d7b8714)
parent 73d6d6d7
...@@ -51,7 +51,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -51,7 +51,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
) )
/** Method to make the variantcalling namespace of shiva */ /** Method to make the variantcalling namespace of shiva */
def makeVariantcalling(multisample: Boolean = false): ShivaVariantcalling with QScript = { def makeVariantcalling(multisample: Boolean, sample: Option[String] = None, library: Option[String] = None): ShivaVariantcalling with QScript = {
if (multisample) new ShivaVariantcalling(qscript) { if (multisample) new ShivaVariantcalling(qscript) {
override def namePrefix = "multisample" override def namePrefix = "multisample"
override def configNamespace: String = "shivavariantcalling" override def configNamespace: String = "shivavariantcalling"
...@@ -59,6 +59,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -59,6 +59,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
} }
else new ShivaVariantcalling(qscript) { else new ShivaVariantcalling(qscript) {
override def configNamespace = "shivavariantcalling" override def configNamespace = "shivavariantcalling"
sampleId = sample
libId = library
} }
} }
...@@ -104,7 +106,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -104,7 +106,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
lazy val variantcalling = if (config("library_variantcalling", default = false).asBoolean && lazy val variantcalling = if (config("library_variantcalling", default = false).asBoolean &&
(bamFile.isDefined || preProcessBam.isDefined)) { (bamFile.isDefined || preProcessBam.isDefined)) {
Some(makeVariantcalling(multisample = false)) Some(makeVariantcalling(multisample = false, sample = Some(sampleId), library = Some(libId)))
} else None } else None
/** This will add jobs for this library */ /** This will add jobs for this library */
...@@ -132,7 +134,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra ...@@ -132,7 +134,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
} }
lazy val variantcalling = if (config("single_sample_variantcalling", default = false).asBoolean) { lazy val variantcalling = if (config("single_sample_variantcalling", default = false).asBoolean) {
Some(makeVariantcalling(multisample = false)) Some(makeVariantcalling(multisample = false, sample = Some(sampleId)))
} else None } else None
override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner) override def keepMergedFiles: Boolean = config("keep_merged_files", default = !useIndelRealigner)
......
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