Commit 4350c5b5 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Adding files to summary json

parent b674053a
......@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFuntion
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
/**
* KrakenReportToJson function class for usage in Biopet pipelines
......
......@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import nl.lumc.sasc.biopet.extensions.tools.{KrakenReportToJson, FastqSync}
import nl.lumc.sasc.biopet.extensions.tools.{ KrakenReportToJson, FastqSync }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -120,11 +120,6 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
krakenReportJSON.skipNames = config("skipNames", default = true)
add(krakenReportJSON)
// val krakenReportJSON = new KrakenReportToJson(qscript)
// krakenReportJSON.input = krakenReport.output
// krakenReportJSON.output = new File(outputDir, s"$outputName.krkn.json")
// add(krakenReportJSON)
addSummaryJobs()
}
......@@ -135,7 +130,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
def summarySettings = Map()
/** Files for the summary */
def summaryFiles = (if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
def summaryFiles: Map[String, File] = Map.empty ++
(if (bamFile.isDefined) Map("input_bam" -> bamFile.get) else Map()) ++
(if (fastqFileR1.isDefined) Map("input_R1" -> fastqFileR1.get) else Map())
}
......
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