Commit ea9fe977 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed executables for summary

parent a61296b2
......@@ -61,17 +61,6 @@ trait SummaryQScript extends BiopetQScript {
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles)
addChecksum(file)
for ((_, sl) <- summarizables) {
for (s <- sl) {
s match {
case c: BiopetCommandLineFunctionTrait => {
executables += c.configName -> (new File(c.executable), c.getVersion)
}
case _ =>
}
}
}
for ((_, file) <- this.summaryFiles)
addChecksum(file)
......
......@@ -48,10 +48,17 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val pipelineMap = {
val files = parseFiles(qscript.summaryFiles)
val settings = qscript.summarySettings
val executables = {
for ((name, (file, version)) <- qscript.executables) yield {
name -> Map("version" -> version, "md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(file.getCanonicalPath, "N/A"))
}
val executables: Map[String, Any] = {
(for (f <- qscript.functions if f.isInstanceOf[BiopetCommandLineFunctionTrait]) yield {
f match {
case f: BiopetCommandLineFunctionTrait => {
f.configName -> Map("version" -> f.getVersion,
"md5" -> BiopetCommandLineFunctionTrait.executableMd5Cache.getOrElse(f.executable, None))
}
case _ => throw new IllegalStateException("This should not be possible")
}
}).toMap
}
val map = Map(qscript.summaryName -> ((if (settings.isEmpty) Map[String, Any]() else Map("settings" -> settings)) ++
......
......@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BwaMem(val root: Configurable) extends Bwa {
......
......@@ -94,7 +94,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
def summaryFiles = Map()
def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1) ++
(if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
def summarySettings = Map(
"skip_metrics" -> skipMetrics,
......
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