diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
index 6dd72260c36889dca3336ca9b7fe0e9d980fbcdd..6664c6be7da2a54aeccf1d274225ff5eac37af43 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
@@ -35,11 +35,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
means we have 2 samples, each with 2 replicates
so our input is a list of lists of Files
*/
- var input: List[List[File]] = List.empty[List[File]]
+ var input: List[List[File]] = Nil
/** input GTF file */
@Input(doc = "Input GTF file", required = true)
- var transcriptsGtf: File = null
+ var transcriptsGtf: File = _
/** output file, computed automatically from output directory */
@Output(doc = "Output CXB file")
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
index 7f30e0bfad6d1a9b3b299fef6fc58e977c87a101..b4b6b3371430d0aa2744e56e9535a5140cd03b31 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
@@ -40,6 +40,8 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction with Versio
object Gzip {
def apply(root: Configurable): Gzip = new Gzip(root)
+ def apply(root: Configurable, input: File, output: File): Gzip = Gzip(root, List(input), output)
+
def apply(root: Configurable, input: List[File], output: File): Gzip = {
val gzip = new Gzip(root)
gzip.input = input
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
new file mode 100644
index 0000000000000000000000000000000000000000..96776a12ec31944feb643bef8226aad0ca49059c
--- /dev/null
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
@@ -0,0 +1,61 @@
+package nl.lumc.sasc.biopet.extensions.centrifuge
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.util.matching.Regex
+
+/**
+ * Created by pjvanthof on 19/09/16.
+ */
+class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with Version {
+ @Input(doc = "Input: FastQ or FastA", required = true)
+ var inputR1: File = _
+
+ @Input(doc = "Input: FastQ or FastA", required = false)
+ var inputR2: Option[File] = None
+
+ var index: File = config("centrifuge_index")
+
+ @Output(doc = "Output with hits per sequence")
+ var output: File = _
+
+ @Output(doc = "Output with hits per sequence")
+ var report: Option[File] = None
+
+ override def defaultThreads = 8
+
+ executable = config("exe", default = "centrifuge", freeVar = false)
+
+ /** Command to get version of executable */
+ def versionCommand: String = s"$executable --version"
+
+ /** Regex to get version from version command output */
+ def versionRegex: Regex = ".* version (.*)".r
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ deps :+= new File(index + ".1.cf")
+ deps :+= new File(index + ".2.cf")
+ deps :+= new File(index + ".3.cf")
+ }
+
+ /**
+ * This function needs to be implemented to define the command that is executed
+ *
+ * @return Command to run
+ */
+ def cmdLine: String = executable +
+ //TODO: Options
+ optional("--threads", threads) +
+ required("-x", index) +
+ (inputR2 match {
+ case Some(r2) => required("-1", inputR1) + required("-2", r2)
+ case _ => required("-U", inputR1)
+ }) +
+ (if (outputAsStsout) "" else required("-S", output)) +
+ optional("--report-file", report)
+}
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
new file mode 100644
index 0000000000000000000000000000000000000000..505d367efb108c9f75e3eeac52719335a1afd624
--- /dev/null
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
@@ -0,0 +1,48 @@
+package nl.lumc.sasc.biopet.extensions.centrifuge
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvanthof on 19/09/16.
+ */
+class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunction {
+ @Input(doc = "Output files centrifuge", required = true)
+ var centrifugeOutputFiles: List[File] = Nil
+
+ @Output(doc = "Output report")
+ var output: File = _
+
+ var index: File = config("centrifuge_index", namespace = "centrifuge")
+
+ var onlyUnique: Boolean = config("only_unique", default = false)
+ var showZeros: Boolean = config("show_zeros", default = false)
+ var isCounts: Boolean = config("is_counts", default = false)
+
+ var minScore: Option[Double] = config("min_score")
+ var minLength: Option[Int] = config("min_length")
+
+ override def defaultCoreMemory = 4.0
+
+ executable = config("exe", default = "centrifuge-kreport", freeVar = false)
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ deps :+= new File(index + ".1.cf")
+ deps :+= new File(index + ".2.cf")
+ deps :+= new File(index + ".3.cf")
+ }
+
+ def cmdLine = executable +
+ conditional(onlyUnique, "--only-unique") +
+ conditional(showZeros, "--show-zeros") +
+ conditional(isCounts, "--is-counts") +
+ optional("--min-score=", minScore, spaceSeparated = false) +
+ optional("--min-length=", minLength, spaceSeparated = false) +
+ required("-x", index) +
+ repeat(centrifugeOutputFiles) +
+ " > " + required(output)
+}
diff --git a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index 2a32e7396eb69a8a4fa955946a68064cf70d4054..989aa8882664d44f2c9bbe40e18f275f8e0dc284 100644
--- a/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
@@ -42,7 +42,7 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFunction wit
@Output(doc = "Output JSON", shortName = "output", required = true)
var output: File = _
- override def defaultCoreMemory = 2.0
+ override def defaultCoreMemory = 4.0
override def cmdLine =
super.cmdLine +
diff --git a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
index 8ef51a20f1c6332294654343015c0d03acd0d50b..99162c95b0d2c7899a5012e94653aa420b9a982c 100644
--- a/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
+++ b/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp
@@ -10,11 +10,13 @@
<%@ var libId: Option[String] = None %>
<%@ var args: Map[String, Any] %>
<%@ var outputDir: File %>
+<%@ var summaryStatsTag: String = "krakenreport" %>
+<%@ var summaryModuleTag: String = "gearskraken" %>
<%
val summaries = if (sampleId.isEmpty && libId.isEmpty) {
- summary.getSampleValues("gearskraken", "stats", "krakenreport").map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
- } else summary.getValue(sampleId, libId, "gearskraken", "stats", "krakenreport").map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
+ summary.getSampleValues(summaryModuleTag, "stats", summaryStatsTag).map(x => x._1 -> x._2.get.asInstanceOf[Map[String, Any]])
+ } else summary.getValue(sampleId, libId, summaryModuleTag, "stats", summaryStatsTag).map(sampleId.get -> _.asInstanceOf[Map[String, Any]]).toList.toMap
val tempFile = File.createTempFile("krona.", ".xml")
tempFile.deleteOnExit()
@@ -24,10 +26,10 @@
args ++ Map("kronaXml" -> tempFile))
- val file = new File(outputDir, "kraken_krona.html")
+ val file = new File(outputDir, s"$summaryModuleTag-$summaryStatsTag.html")
val writer = new PrintWriter(file)
writer.println(output)
writer.close()
%>
-<iframe src="kraken_krona.html" style="width:100%;height:80vh;border:none;"></iframe>
+<iframe src="${summaryModuleTag}-${summaryStatsTag}.html" style="width:100%;height:80vh;border:none;"></iframe>
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f0277218c331498389f961dee94fbe67ff019613
--- /dev/null
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
@@ -0,0 +1,76 @@
+package nl.lumc.sasc.biopet.pipelines.gears
+
+import nl.lumc.sasc.biopet.core.SampleLibraryTag
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.Gzip
+import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
+import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 19/09/16.
+ */
+class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
+
+ var fastqR1: File = _
+
+ var fastqR2: Option[File] = None
+
+ var outputName: String = _
+
+ override def fixedValues = Map("centrifugekreport" -> Map("only_unique" -> false))
+
+ def init(): Unit = {
+ require(fastqR1 != null)
+ require(outputName != null)
+ }
+
+ def centrifugeOutput = new File(outputDir, s"$outputName.centrifuge.gz")
+
+ def biopetScript(): Unit = {
+ val centrifuge = new Centrifuge(this)
+ centrifuge.inputR1 = fastqR1
+ centrifuge.inputR2 = fastqR2
+ centrifuge.output = new File(outputDir, s"$outputName.centrifuge")
+ centrifuge.report = Some(new File(outputDir, s"$outputName.centrifuge.report"))
+ centrifuge.isIntermediate = true
+ add(centrifuge)
+
+ add(Gzip(this, centrifuge.output, centrifugeOutput))
+
+ makeKreport(List(centrifuge.output), "centrifuge", unique = false)
+ makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)
+
+ addSummaryJobs()
+ }
+
+ protected def makeKreport(inputFiles: List[File], name: String, unique: Boolean): Unit = {
+ val centrifugeKreport = new CentrifugeKreport(this)
+ centrifugeKreport.centrifugeOutputFiles = inputFiles
+ centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
+ centrifugeKreport.onlyUnique = unique
+ add(centrifugeKreport)
+
+ val krakenReportJSON = new KrakenReportToJson(this)
+ krakenReportJSON.inputReport = centrifugeKreport.output
+ krakenReportJSON.output = new File(outputDir, s"$outputName.$name.krkn.json")
+ krakenReportJSON.skipNames = config("skipNames", default = false)
+ add(krakenReportJSON)
+ addSummarizable(krakenReportJSON, s"${name}_report")
+ }
+
+ /** Location of summary file */
+ def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".centrifuge.summary.json")
+
+ /** Pipeline settings shown in the summary file */
+ def summarySettings: Map[String, Any] = Map()
+
+ /** Statistics shown in the summary file */
+ def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1, "centrifuge_output" -> centrifugeOutput) ++
+ (fastqR2 match {
+ case Some(file) => Map("input_R2" -> file)
+ case _ => Map()
+ })
+
+}
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
index e4e5852b74b287ea80e8ed1e2afbff60f25caf86..384d5ba11aa70a98287757759b94dd9fedca2c9f 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
def init(): Unit = {
require(fastqR1 != null)
- if (outputName == null) outputName = fastqR1.getName
- .stripSuffix(".gz")
- .stripSuffix(".fq")
- .stripSuffix(".fastq")
+ require(outputName != null)
}
lazy val krakenConvertToFasta: Boolean = config("kraken_discard_quality", default = false)
@@ -107,7 +104,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".kraken.summary.json")
/** Pipeline settings shown in the summary file */
- def summarySettings: Map[String, Any] = Map.empty
+ def summarySettings: Map[String, Any] = Map()
/** Statistics shown in the summary file */
def summaryFiles: Map[String, File] = outputFiles + ("input_R1" -> fastqR1) ++ (fastqR2 match {
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index d28668c484e60ce3aaf781fb974fffd16651477e..0a295008278929e07bd629f1211e32298a989a9d 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -38,13 +38,20 @@ object GearsReport extends MultisampleReportBuilder {
def indexPage = {
val krakenExecuted = summary.getSampleValues("gearskraken", "stats", "krakenreport").values.forall(_.isDefined)
+ val centrifugeExecuted = summary.getSampleValues("gearscentrifuge", "stats", "centrifuge_report").values.forall(_.isDefined)
val qiimeClosesOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_closed_otu_table", "path")
.map(x => new File(x.toString))
val qiimeOpenOtuTable = summary.getValue("gears", "files", "pipeline", "qiime_open_otu_table", "path")
.map(x => new File(x.toString))
ReportPage(
- (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
+ (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_report")
+ )), Map())), List(
+ "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_unique_report")
+ )), Map("summaryModuleTag" -> "gearscentrifuge")))
+ else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> ReportPage(List(), List(
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
@@ -74,12 +81,19 @@ object GearsReport extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
val krakenExecuted = summary.getValue(Some(sampleId), None, "gearskraken", "stats", "krakenreport").isDefined
+ val centrifugeExecuted = summary.getValue(Some(sampleId), None, "gearscentrifuge", "stats", "centrifuge_report").isDefined
val qiimeClosesOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
.map(x => new File(x.toString))
val qiimeOpenOtuTable = summary.getValue(Some(sampleId), None, "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
.map(x => new File(x.toString))
- ReportPage((if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+ ReportPage((if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_report")
+ )), Map())), List(
+ "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_unique_report")
+ )), Map("summaryModuleTag" -> "gearscentrifuge")))
+ else Nil) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
@@ -99,6 +113,7 @@ object GearsReport extends MultisampleReportBuilder {
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gearskraken", "stats", "krakenreport").isDefined
+ val centrifugeExecuted = summary.getValue(Some(sampleId), Some(libId), "gearscentrifuge", "stats", "centrifuge_report").isDefined
val qiimeClosesOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeclosed", "files", "pipeline", "otu_table", "path")
.map(x => new File(x.toString))
val qiimeOpenOtuTable = summary.getValue(Some(sampleId), Some(libId), "gearsqiimeopen", "files", "pipeline", "otu_table", "path")
@@ -106,7 +121,13 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
- ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+ ) ::: (if (centrifugeExecuted) List("Centriguge analysis" -> ReportPage(List("Non-unique" -> ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_report")
+ )), Map())), List(
+ "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
+ Map("summaryStatsTag" -> "centrifuge_unique_report")
+ )), Map("summaryModuleTag" -> "gearscentrifuge")))
+ else Nil) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index 60e72489ca37dbfbb5d5d3ffbaca10a1c9c3f313..f05760f994e1b60643a9a3599afdd23ca1549cae 100644
--- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -41,6 +41,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
var outputName: String = _
lazy val krakenScript = if (config("gears_use_kraken", default = true)) Some(new GearsKraken(this)) else None
+ lazy val centrifugeScript = if (config("gears_use_centrifuge", default = false)) Some(new GearsCentrifuge(this)) else None
lazy val qiimeRatx = if (config("gears_use_qiime_rtax", default = false)) Some(new GearsQiimeRtax(this)) else None
lazy val qiimeClosed = if (config("gears_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this)) else None
lazy val qiimeOpen = if (config("gears_use_qiime_open", default = false)) Some(new GearsQiimeOpen(this)) else None
@@ -126,6 +127,14 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
add(kraken)
}
+ centrifugeScript foreach { centrifuge =>
+ centrifuge.outputDir = new File(outputDir, "centrifuge")
+ centrifuge.fastqR1 = r1
+ centrifuge.fastqR2 = r2
+ centrifuge.outputName = outputName
+ add(centrifuge)
+ }
+
qiimeRatx foreach { qiimeRatx =>
qiimeRatx.outputDir = new File(outputDir, "qiime_rtax")
qiimeRatx.fastqR1 = r1
diff --git a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
index 31ffcab22c517a62264166c95564081aa431b6cc..6d9f953edd8a4a819288d3a95326ab1e446cbdb3 100644
--- a/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+++ b/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
@@ -17,6 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File
import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.BiopetPipe
+import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -49,6 +51,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
def paired: Boolean = false
def hasOutputName: Boolean = false
def kraken: Option[Boolean] = None
+ def centrifuge: Boolean = false
def qiimeClosed: Boolean = false
def qiimeOpen: Boolean = false
def qiimeRtax: Boolean = false
@@ -61,6 +64,7 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
def testGears(): Unit = {
val map = ConfigUtils.mergeMaps(Map(
"gears_use_qiime_rtax" -> qiimeRtax,
+ "gears_use_centrifuge" -> centrifuge,
"gears_use_qiime_closed" -> qiimeClosed,
"gears_use_qiime_open" -> qiimeOpen,
"gears_use_seq_count" -> seqCount,
@@ -102,12 +106,15 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")
}
+ val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
+
gears.summarySettings("gears_use_kraken") shouldBe kraken.getOrElse(true)
gears.summarySettings("gear_use_qiime_rtax") shouldBe qiimeRtax
gears.summarySettings("gear_use_qiime_closed") shouldBe qiimeClosed
gears.summarySettings("gear_use_qiime_open") shouldBe qiimeOpen
gears.krakenScript.isDefined shouldBe kraken.getOrElse(true)
+ gears.centrifugeScript.isDefined shouldBe centrifuge
gears.qiimeClosed.isDefined shouldBe qiimeClosed
gears.qiimeOpen.isDefined shouldBe qiimeOpen
gears.qiimeRatx.isDefined shouldBe qiimeRtax
@@ -119,7 +126,11 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears.functions.count(_.isInstanceOf[Kraken]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
gears.functions.count(_.isInstanceOf[KrakenReport]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
- gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe (if (kraken.getOrElse(true)) 1 else 0)
+ gears.functions.count(_.isInstanceOf[KrakenReportToJson]) shouldBe
+ ((if (kraken.getOrElse(true)) 1 else 0) + (if (centrifuge) 2 else 0))
+
+ gears.functions.count(_.isInstanceOf[Centrifuge]) shouldBe (if (centrifuge) 1 else 0)
+ gears.functions.count(_.isInstanceOf[CentrifugeKreport]) shouldBe (if (centrifuge) 2 else 0)
}
}
}
@@ -132,6 +143,9 @@ class GearsSingleDefaultTest extends TestGearsSingle
class GearsSingleKrakenTest extends TestGearsSingle {
override def kraken = Some(true)
}
+class GearsSingleCentrifugeTest extends TestGearsSingle {
+ override def centrifuge = true
+}
class GearsSingleQiimeClosedTest extends TestGearsSingle {
override def qiimeClosed = true
}
@@ -149,6 +163,10 @@ class GearsSingleKrakenPairedTest extends TestGearsSingle {
override def paired = true
override def kraken = Some(true)
}
+class GearsSingleCentrifugePairedTest extends TestGearsSingle {
+ override def paired = true
+ override def centrifuge = true
+}
class GearsSingleQiimeClosedPairedTest extends TestGearsSingle {
override def paired = true
override def qiimeClosed = true
@@ -168,6 +186,7 @@ class GearsSingleseqCountPairedTest extends TestGearsSingle {
class GearsSingleAllTest extends TestGearsSingle {
override def kraken = Some(true)
+ override def centrifuge = true
override def qiimeClosed = true
override def qiimeOpen = true
override def qiimeRtax = true
@@ -175,6 +194,7 @@ class GearsSingleAllTest extends TestGearsSingle {
}
class GearsSingleAllPairedTest extends TestGearsSingle {
override def kraken = Some(true)
+ override def centrifuge = true
override def qiimeClosed = true
override def qiimeOpen = true
override def qiimeRtax = true
@@ -214,6 +234,8 @@ object TestGearsSingle {
val executables = Map(
"kraken" -> Map("exe" -> "test", "db" -> "test"),
+ "centrifuge" -> Map("exe" -> "test", "centrifuge_index" -> "test"),
+ "centrifugekreport" -> Map("exe" -> "test"),
"krakenreport" -> Map("exe" -> "test", "db" -> "test"),
"sambamba" -> Map("exe" -> "test"),
"samtools" -> Map("exe" -> "test"),