From eebab126a20caa960a3e40ef490793aa801a78a5 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Wed, 27 Jan 2016 16:16:44 +0100
Subject: [PATCH] Pindel update wrapper, specifing the output files (pindel
generates more files)
---
.../extensions/pindel/PindelCaller.scala | 32 +++++++++++++++++++
.../biopet/extensions/pindel/PindelVCF.scala | 12 ++++---
.../pipelines/shiva/svcallers/Pindel.scala | 10 ++++--
3 files changed, 48 insertions(+), 6 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index f0bc396a3..426dd52dd 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -59,6 +59,21 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
@Output(doc = "Output file of pindel, pointing to the DEL file")
var outputFile: File = _
+ @Output(doc="", required=false)
+ var outputINV: File = _
+ @Output(doc="", required=false)
+ var outputTD: File = _
+ @Output(doc="", required=false)
+ var outputLI: File = _
+ @Output(doc="", required=false)
+ var outputBP: File = _
+ @Output(doc="", required=false)
+ var outputSI: File = _
+ @Output(doc="", required=false)
+ var outputRP: File = _
+ @Output(doc="", required=false)
+ var outputCloseEndMapped: File = _
+
var RP: Option[Int] = config("RP")
var minDistanceToTheEnd: Option[Int] = config("min_distance_to_the_end")
// var threads
@@ -126,6 +141,23 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
}
}
+ /** setting the output files for the many outputfiles pindel has */
+
+ outputINV = new File(outputPrefix + File.separator, "sample_INV")
+ outputTD = new File(outputPrefix + File.separator, "sample_TD")
+ if (reportLongInsertions) {
+ outputLI = new File(outputPrefix + File.separator, "sample_LI")
+ }
+ if (reportBreakpoints){
+ outputBP = new File(outputPrefix + File.separator, "sample_BP")
+ }
+ outputSI = new File(outputPrefix + File.separator, "sample_SI")
+
+ outputRP = new File(outputPrefix + File.separator, "sample_RP")
+ if (reportCloseMappedReads) {
+ outputCloseEndMapped = new File(outputPrefix + File.separator, "sample_CloseEndMapped")
+ }
+
// set the output file, the DELetion call is always made
// TODO: add more outputs for the LI, SI, INV etc...
outputFile = new File(outputPrefix + File.separator, "sample_D")
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
index 8b257bd4e..6d69531e8 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala
@@ -15,8 +15,8 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
override def defaultCoreMemory = 2.0
override def defaultThreads = 1
- def versionRegex = """Version:? (.*)""".r
- override def versionExitcode = List(1)
+ def versionRegex = """Version:?[ ]+(.*)""".r
+ override def versionExitcode = List(0)
def versionCommand = executable + " -h"
/**
@@ -28,12 +28,15 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
@Output
var outputVCF: File = _
- var referenceDate: String = config("reference_date", freeVar = false)
+ var rDate: String = config("rdate", freeVar = false)
override def beforeGraph: Unit = {
if (reference == null) reference = referenceFasta()
}
+ @Input
+ var pindelOutputInputHolder: File = _
+
var pindelOutput: Option[File] = config("pindel_output")
var pindelOutputRoot: Option[File] = config("pindel_output_root")
var chromosome: Option[String] = config("chromosome")
@@ -60,8 +63,9 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
var gatkCompatible: Boolean = config("gatk_compatible", default = false)
def cmdLine = required(executable) +
+ required("--reference", reference) +
required("--reference_name", referenceSpecies) +
- required("--reference_date", referenceDate) +
+ required("--reference_date", rDate) +
optional("--pindel_output", pindelOutput) +
optional("--pindel_output_root", pindelOutputRoot) +
required("--vcf", outputVCF) +
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index ee4d8289b..a318c5eb9 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -29,6 +29,11 @@ class Pindel(val root: Configurable) extends SvCaller {
def this() = this(null)
+ /** Default pipeline config */
+ override def defaults = Map("pindelvcf" -> Map(
+ "rdate" -> new SimpleDateFormat("yyyyMMdd").format(Calendar.getInstance().getTime())
+ ))
+
def biopetScript() {
for ((sample, bamFile) <- inputBams) {
val pindelDir = new File(outputDir, sample)
@@ -51,8 +56,9 @@ class Pindel(val root: Configurable) extends SvCaller {
val todayformat = new SimpleDateFormat("yyyyMMdd")
val pindelVcf = new PindelVCF(this)
- pindelVcf.pindelOutputRoot = Some(pindelDir)
- pindelVcf.referenceDate = todayformat.format(today) // officially, we should enter the date of the genome here
+ pindelVcf.pindelOutputInputHolder = pindel.outputFile
+ pindelVcf.pindelOutputRoot = Some(new File(pindelDir, "sample"))
+ pindelVcf.rDate = todayformat.format(today) // officially, we should enter the date of the genome here
pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
add(pindelVcf)
}
--
GitLab