Commit ff8bbecb authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style changes

parent ea2bdb56
......@@ -2,23 +2,23 @@ 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.{Cutadapt, Flash}
import nl.lumc.sasc.biopet.extensions.{ Cutadapt, Flash }
import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 29/12/15.
*/
* Created by pjvanthof on 29/12/15.
*/
class CombineReads(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
var fastqR1: File = _
@Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
var fastqR2: File = _
override def fixedValues = Map("flash" -> Map("compress" -> true))
/** Init for pipeline */
def init(): Unit = {
}
......@@ -27,7 +27,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
private lazy val forwardPrimers: List[String] = config("forward_primers")
private lazy val reversePrimers: List[String] = config("reverse_primers")
def combinedFastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
swapExt(outputDir, flash.combinedFastq, ".fastq.gz", ".clip.fastq.gz")
else flash.combinedFastq
......@@ -57,7 +57,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
add(cutadapt)
addSummarizable(cutadapt, "cutadapt")
}
val combinedFastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "combined_fastqc"))
add(combinedFastqc)
addSummarizable(combinedFastqc, "fastqc_combined")
......
......@@ -156,9 +156,9 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** File to put in the summary for thie pipeline */
def summaryFiles: Map[String, File] = (
qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
).toMap
qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
).toMap
}
object Gears extends PipelineCommand
\ No newline at end of file
......@@ -127,11 +127,11 @@ object GearsKraken {
if (k == "root") {
val unclassified = summaries(sample)("unclassified").asInstanceOf[Map[String, Any]]("size").asInstanceOf[Long]
<val>
{getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified}
{ getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified }
</val>
} else {
<val>
{getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0)}
{ getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0) }
</val>
}
}
......
......@@ -59,7 +59,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
def summarySettings: Map[String, Any] = Map()
/** File to put in the summary for thie pipeline */
def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable,"otu_map" -> otuMap)
def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable, "otu_map" -> otuMap)
/** Name of summary output file */
def summaryFile: File = new File(outputDir, "summary.closed_reference.json")
......
......@@ -80,7 +80,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
) ::: (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(
......
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.{BiopetQScript, SampleLibraryTag}
import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/29/15.
*/
* Created by pjvan_thof on 12/29/15.
*/
class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
var fastqInput: File = _
......
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