From f7ea04a735ea13d5a6ae7433dc74cefcfad9fb2b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 12:40:47 +0200
Subject: [PATCH] Use piping after bwamem
---
.../extensions/samtools/SamtoolsSort.scala | 6 +++---
.../biopet/pipelines/mapping/Mapping.scala | 18 +++++++++++++-----
2 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
index d2f723f9e..fee7906d2 100644
--- a/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala
@@ -16,9 +16,9 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
@Output
var output: File = _
- val compresion: Option[Int] = config("l")
- val outputFormat: Option[String] = config("O")
- val sortByName: Boolean = config("sort_by_name", default = false)
+ var compresion: Option[Int] = config("l")
+ var outputFormat: Option[String] = config("O")
+ var sortByName: Boolean = config("sort_by_name", default = false)
val prefix: String = config("prefix", default = new File(qSettings.tempDirectory, output.getAbsolutePath))
def cmdLine = optional("-m", (coreMemeory + "G")) +
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 9d508b12c..24ec2a2bb 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -19,6 +19,7 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsSort
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
@@ -331,11 +332,18 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
bwaCommand.R = Some(getReadGroupBwa)
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
bwaCommand.isIntermediate = true
- add(bwaCommand)
- val sortSam = SortSam(this, bwaCommand.output, output)
- if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
- add(sortSam)
- sortSam.output
+ if (config("use_pipes", default = true).asBoolean) {
+ val samtoolsSort = new SamtoolsSort(this)
+ samtoolsSort.outputFormat = Some("bam")
+ samtoolsSort.output = output
+ add(bwaCommand | samtoolsSort)
+ } else {
+ add(bwaCommand)
+ val sortSam = SortSam(this, bwaCommand.output, output)
+ if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+ add(sortSam)
+ }
+ output
}
def addGsnap(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
--
GitLab