From 03c15ef352d4459f83692c0230e47e32a0660d92 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 29 Dec 2015 13:06:45 +0100
Subject: [PATCH] Added combine reads for GearsSingle
---
.../biopet/pipelines/gears/CombineReads.scala | 48 +++++++++++++++++--
.../biopet/pipelines/gears/GearsSingle.scala | 12 ++---
2 files changed, 51 insertions(+), 9 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
index a6c269b7b..cd14d2323 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
@@ -2,7 +2,8 @@ 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.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
@@ -15,18 +16,59 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
@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 = {
}
+ private lazy val flash = new Flash(this)
+
+ 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
+
+ def notCombinedR1Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
+ swapExt(outputDir, flash.notCombinedR1, ".fastq.gz", ".clip.fastq.gz")
+ else flash.notCombinedR1
+
+ def notCombinedR2Fastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
+ swapExt(outputDir, flash.notCombinedR2, ".fastq.gz", ".clip.fastq.gz")
+ else flash.notCombinedR2
+
/** Pipeline itself */
def biopetScript(): Unit = {
- val flash = new Flash(this)
flash.outputDirectory = new File(outputDir, "flash")
flash.fastqR1 = fastqR1
flash.fastqR2 = fastqR2
+ flash.isIntermediate = (forwardPrimers ::: reversePrimers).nonEmpty
add(flash)
+
+ if ((forwardPrimers ::: reversePrimers).nonEmpty) {
+ val cutadapt = new Cutadapt(this)
+ cutadapt.fastq_input = flash.combinedFastq
+ cutadapt.fastq_output = this.combinedFastq
+ cutadapt.stats_output = swapExt(outputDir, cutadapt.fastq_output, ".fastq.gz", ".stats")
+ cutadapt.opt_anywhere ++= (forwardPrimers ::: reversePrimers)
+ add(cutadapt)
+ addSummarizable(cutadapt, "cutadapt")
+ }
+
+ val combinedFastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "combined_fastqc"))
+ add(combinedFastqc)
+ addSummarizable(combinedFastqc, "fastqc_combined")
+
+ val notCombinedR1Fastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "not_combined_R1_fastqc"))
+ add(notCombinedR1Fastqc)
+ addSummarizable(notCombinedR1Fastqc, "fastqc_not_combined_R1")
+
+ val notCombinedR2Fastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "not_combined_R2_fastqc"))
+ add(notCombinedR2Fastqc)
+ addSummarizable(notCombinedR2Fastqc, "fastqc_not_combined_R2")
}
/** Must return a map with used settings for this pipeline */
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 0cf2d0f00..f94fe96e2 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
@@ -104,12 +104,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
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
+ val combineReads = new CombineReads(this)
+ combineReads.outputDir = new File(outputDir, "combine_reads")
+ combineReads.fastqR1 = r1
+ combineReads.fastqR2 = r2
+ add(combineReads)
+ combineReads.combinedFastq
case _ => r1
}
}
--
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