From b5c6727b6058f36aa008076117e6c13b71618c98 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 29 Dec 2015 11:00:20 +0100
Subject: [PATCH] Moved flash as general job
---
.../pipelines/gears/GearsQiimeClosed.scala | 19 +++----------------
.../biopet/pipelines/gears/GearsSingle.scala | 17 +++++++++++++++--
2 files changed, 18 insertions(+), 18 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
index dae73af73..f78a7f207 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
@@ -19,9 +19,7 @@ import scala.xml.{ PrettyPrinter, Elem }
*/
class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
- var fastqR1: File = _
-
- var fastqR2: Option[File] = None
+ var fastqInput: File = _
override def defaults = Map(
"splitlibrariesfastq" -> Map(
@@ -30,7 +28,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
)
def init() = {
- require(fastqR1 != null)
+ require(fastqInput != null)
}
private var _otuMap: File = _
@@ -41,19 +39,8 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
def biopetScript() = {
- val fastqFile = fastqR2 match {
- case Some(r2) =>
- val flash = new Flash(this)
- flash.outputDirectory = new File(outputDir, "combine_reads_flash")
- flash.fastqR1 = fastqR1
- flash.fastqR2 = r2
- add(flash)
- flash.combinedFastq
- case _ => fastqR1
- }
-
val splitLib = new SplitLibrariesFastq(this)
- splitLib.input :+= fastqFile
+ splitLib.input :+= fastqInput
splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
sampleId.foreach(splitLib.sample_ids :+= _)
add(splitLib)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
index e966e2371..0cf2d0f00 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.Flash
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -100,6 +101,19 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case _ => throw new IllegalArgumentException("Missing input files")
}
+ lazy val combinedFastq = {
+ r2 match {
+ case Some(r2) =>
+ val flash = new Flash(this)
+ flash.outputDirectory = new File(outputDir, "combine_reads_flash")
+ flash.fastqR1 = r1
+ flash.fastqR2 = r2
+ add(flash)
+ flash.combinedFastq
+ case _ => r1
+ }
+ }
+
krakenScript foreach { kraken =>
kraken.outputDir = new File(outputDir, "kraken")
kraken.fastqR1 = r1
@@ -117,8 +131,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeClosed foreach { qiimeClosed =>
qiimeClosed.outputDir = new File(outputDir, "qiime_closed")
- qiimeClosed.fastqR1 = r1
- qiimeClosed.fastqR2 = r2
+ qiimeClosed.fastqInput = combinedFastq
add(qiimeClosed)
//TODO: Plots
--
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