diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala index 034a6e57b743bb3f3648a0138354bd3299da646f..0e14359fd649a6d1d56ec5c3aea23fc53f1cbec7 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala @@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears import htsjdk.samtools.SamReaderFactory import nl.lumc.sasc.biopet.FullVersion -import nl.lumc.sasc.biopet.core.{PipelineCommand, MultiSampleQScript} +import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript } import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.extensions.Ln import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport } @@ -58,9 +58,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs def summaryFile = new File(outputDir, "gears.summary.json") /** Settings of pipeline for summary */ - def summarySettings = Map( - "version" -> FullVersion - ) + def summarySettings = Map() /** Files for the summary */ def summaryFiles = Map() @@ -294,18 +292,18 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs qscript.add(samToFastq) // sync the fastq records - val fastqsync = new FastqSync(qscript) - fastqsync.refFastq = samToFastq.fastqR1 - fastqsync.inputFastq1 = samToFastq.fastqR1 - fastqsync.inputFastq2 = samToFastq.fastqR2 - fastqsync.outputFastq1 = createFile(".unmapsynced.R1.fastq.gz") - fastqsync.outputFastq2 = createFile(".unmapsynced.R2.fastq.gz") - fastqsync.outputStats = createFile(".syncstats.json") - qscript.add(fastqsync) + val fastqSync = new FastqSync(qscript) + fastqSync.refFastq = samToFastq.fastqR1 + fastqSync.inputFastq1 = samToFastq.fastqR1 + fastqSync.inputFastq2 = samToFastq.fastqR2 + fastqSync.outputFastq1 = createFile(".unmapsynced.R1.fastq.gz") + fastqSync.outputFastq2 = createFile(".unmapsynced.R2.fastq.gz") + fastqSync.outputStats = createFile(".syncstats.json") + qscript.add(fastqSync) // start kraken val krakenAnalysis = new Kraken(qscript) - krakenAnalysis.input = List(fastqsync.outputFastq1, fastqsync.outputFastq2) + krakenAnalysis.input = List(fastqSync.outputFastq1, fastqSync.outputFastq2) krakenAnalysis.output = createFile(".krkn.raw") krakenAnalysis.paired = true krakenAnalysis.classified_out = Option(createFile(".krkn.classified.fastq")) @@ -319,7 +317,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs krakenReport.show_zeros = true krakenReport.output = createFile(".krkn.full") qscript.add(krakenReport) - } } }