Commit e667ee49 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Review changes

parent bc53f7e3
...@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears ...@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import htsjdk.samtools.SamReaderFactory import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.FullVersion 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.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport } import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
...@@ -58,9 +58,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs ...@@ -58,9 +58,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
def summaryFile = new File(outputDir, "gears.summary.json") def summaryFile = new File(outputDir, "gears.summary.json")
/** Settings of pipeline for summary */ /** Settings of pipeline for summary */
def summarySettings = Map( def summarySettings = Map()
"version" -> FullVersion
)
/** Files for the summary */ /** Files for the summary */
def summaryFiles = Map() def summaryFiles = Map()
...@@ -294,18 +292,18 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs ...@@ -294,18 +292,18 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
qscript.add(samToFastq) qscript.add(samToFastq)
// sync the fastq records // sync the fastq records
val fastqsync = new FastqSync(qscript) val fastqSync = new FastqSync(qscript)
fastqsync.refFastq = samToFastq.fastqR1 fastqSync.refFastq = samToFastq.fastqR1
fastqsync.inputFastq1 = samToFastq.fastqR1 fastqSync.inputFastq1 = samToFastq.fastqR1
fastqsync.inputFastq2 = samToFastq.fastqR2 fastqSync.inputFastq2 = samToFastq.fastqR2
fastqsync.outputFastq1 = createFile(".unmapsynced.R1.fastq.gz") fastqSync.outputFastq1 = createFile(".unmapsynced.R1.fastq.gz")
fastqsync.outputFastq2 = createFile(".unmapsynced.R2.fastq.gz") fastqSync.outputFastq2 = createFile(".unmapsynced.R2.fastq.gz")
fastqsync.outputStats = createFile(".syncstats.json") fastqSync.outputStats = createFile(".syncstats.json")
qscript.add(fastqsync) qscript.add(fastqSync)
// start kraken // start kraken
val krakenAnalysis = new Kraken(qscript) 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.output = createFile(".krkn.raw")
krakenAnalysis.paired = true krakenAnalysis.paired = true
krakenAnalysis.classified_out = Option(createFile(".krkn.classified.fastq")) krakenAnalysis.classified_out = Option(createFile(".krkn.classified.fastq"))
...@@ -319,7 +317,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs ...@@ -319,7 +317,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
krakenReport.show_zeros = true krakenReport.show_zeros = true
krakenReport.output = createFile(".krkn.full") krakenReport.output = createFile(".krkn.full")
qscript.add(krakenReport) qscript.add(krakenReport)
} }
} }
} }
......
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