From 76da88831f060eaf7171e63875d11b660adb76ca Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 15 Oct 2015 17:20:25 +0200
Subject: [PATCH] added proper piping to bcftools and mpileup. [GENTRAP VARSCAN
SHOULD BE TESTED]
---
.../extensions/bcftools/BcftoolsCall.scala | 56 ++++++++++++++++---
.../extensions/samtools/SamtoolsMpileup.scala | 11 ++--
.../extensions/tools/MpileupToVcf.scala | 29 +++-------
.../gentrap/extensions/CustomVarScan.scala | 4 +-
.../shiva/ShivaVariantcallingTrait.scala | 42 +++++---------
5 files changed, 77 insertions(+), 65 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
index 537cd377d..8b721d36a 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
@@ -22,28 +22,66 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** This extension is based on bcftools 1.1-134 */
class BcftoolsCall(val root: Configurable) extends Bcftools {
- @Input(doc = "Input File")
+ @Input(doc = "Input File", required = false)
var input: File = _
- @Output(doc = "output File")
+ @Output(doc = "output File", required = false)
var output: File = _
- var O: String = null
- var v: Boolean = config("v", default = true)
+ var O: Option[String] = None
+ var v: Boolean = config("v", default = false)
var c: Boolean = config("c", default = false)
var m: Boolean = config("m", default = false)
+ var r: Option[String] = config("r")
+ @Input(required = false)
+ var R: Option[String] = config("R")
+ var s: Option[String] = config("s")
+ @Input(required = false)
+ var S: Option[File] = config("S")
+ var t: Option[String] = config("t")
+ @Input(required = false)
+ var T: Option[String] = config("T")
+ var A: Boolean = config("A", default = false)
+ var f: List[String] = config("f", default = Nil)
+ var g: Option[Int] = config("g")
+ var i: Boolean = config("i", default = false)
+ var M: Boolean = config("M", default = false)
+ var V: Option[String] = config("V")
+ var C: Option[String] = config("C")
+ var n: Option[Float] = config("n")
+ var p: Option[Float] = config("p")
+ var P: Option[Float] = config("P")
+ var X: Boolean = config("X", default = false)
+ var Y: Boolean = config("Y", default = false)
override def beforeGraph(): Unit = {
require(c != m)
}
- def cmdBase = required(executable) +
+ def cmdLine = required(executable) +
required("call") +
optional("-O", O) +
conditional(v, "-v") +
conditional(c, "-c") +
- conditional(m, "-m")
- def cmdPipeInput = cmdBase + "-"
- def cmdPipe = cmdBase + input
- def cmdLine = cmdPipe + " > " + required(output)
+ conditional(m, "-m") +
+ optional("-r", r) +
+ optional("-R", R) +
+ optional("-s", s) +
+ optional("-S", S) +
+ optional("-t", t) +
+ optional("-T", T) +
+ conditional(A, "-A") +
+ repeat("-f", f) +
+ optional("-g", g) +
+ conditional(i, "-i") +
+ conditional(M, "-M") +
+ optional("-V", V) +
+ optional("-C", C) +
+ optional("-n", n) +
+ optional("-p", p) +
+ optional("-P", P) +
+ conditional(X, "-X") +
+ conditional(Y, "-Y") +
+ (if (outputAsStsout) "" else required("-o", output)) +
+ (if (inputAsStdin) "-" else required(input))
}
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
index 449b49cf0..02ded651d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
@@ -47,7 +47,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools with Reference {
reference = referenceFasta()
}
- def cmdBase = required(executable) +
+ def cmdLine = required(executable) +
required("mpileup") +
optional("-f", reference) +
optional("-l", intervalBed) +
@@ -56,12 +56,9 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools with Reference {
optional("-d", depth) +
conditional(outputMappingQuality, "-s") +
conditional(disableBaq, "-B") +
- conditional(u, "-u")
- def cmdPipeInput = cmdBase + "-"
- def cmdPipe = cmdBase + repeat(input)
-
- /** Returns command to execute */
- def cmdLine = cmdPipe + " > " + required(output)
+ conditional(u, "-u") +
+ (if (outputAsStsout) "" else required("-o", output)) +
+ (if (inputAsStdin) "-" else repeat(input))
}
object SamtoolsMpileup {
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
index 60797ce9c..27e7ce903 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -47,12 +47,9 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
override def defaultCoreMemory = 3.0
- override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
- super.defaults)
-
override def beforeGraph() {
super.beforeGraph()
- reference = referenceFasta().getAbsolutePath
+ if (reference == null) reference = referenceFasta().getAbsolutePath
val samtoolsMpileup = new SamtoolsMpileup(this)
}
@@ -66,20 +63,12 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
}
- override def cmdLine = {
- (if (inputMpileup == null) {
- val samtoolsMpileup = new SamtoolsMpileup(this)
- samtoolsMpileup.reference = referenceFasta()
- samtoolsMpileup.input = List(inputBam)
- samtoolsMpileup.cmdPipe + " | "
- } else "") +
- super.cmdLine +
- required("-o", output) +
- optional("--minDP", minDP) +
- optional("--minAP", minAP) +
- optional("--homoFraction", homoFraction) +
- optional("--ploidy", ploidy) +
- required("--sample", sample) +
- (if (inputBam == null) required("-I", inputMpileup) else "")
- }
+ override def cmdLine = super.cmdLine +
+ required("-o", output) +
+ optional("--minDP", minDP) +
+ optional("--minAP", minAP) +
+ optional("--homoFraction", homoFraction) +
+ optional("--ploidy", ploidy) +
+ required("--sample", sample) +
+ (if (inputAsStdin) "" else required("-I", inputMpileup))
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index 8871f481f..f2f11a03e 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -48,6 +48,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction wi
disableBaq = true
depth = Option(1000000)
outputMappingQuality = true
+
}
private def fixMpileup = new PythonCommandLineFunction {
@@ -96,7 +97,6 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction wi
def cmdLine: String = {
// FIXME: manual trigger of commandLine for version retrieval
mpileup.commandLine
- mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile().commandLine + " | " +
- varscan.commandLine + " && " + compress.commandLine + " && " + index.commandLine
+ (mpileup | fixMpileup | removeEmptyPile() | varscan).commandLine + " && " + compress.commandLine + " && " + index.commandLine
}
}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index cdf358e97..985d75879 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -48,6 +48,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
}
}
+ override def defaults = Map("bcftoolscall" -> Map("f" -> List("GQ")))
+
/** Executed before script */
def init(): Unit = {
}
@@ -165,20 +167,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
mp.reference = referenceFasta()
val bt = new BcftoolsCall(qscript)
- bt.O = "z"
+ bt.O = Some("z")
bt.v = true
bt.c = true
- //TODO: add proper class with piping support, see also issue #114
- add(new CommandLineFunction {
- @Input
- var input = inputBams
-
- @Output
- var output = outputFile
-
- def commandLine: String = mp.cmdPipe + " | " + bt.cmdPipeInput + " > " + outputFile + " && tabix -p vcf " + outputFile
- })
+ add(mp | bt > outputFile)
}
}
@@ -195,27 +188,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
val mp = new SamtoolsMpileup(qscript)
mp.input :+= inputBam
mp.u = true
- //TODO: proper piping should be implemented
mp.reference = referenceFasta()
val bt = new BcftoolsCall(qscript)
- bt.O = "z"
+ bt.O = Some("z")
bt.v = true
bt.c = true
+ bt.output = new File(outputDir, inputBam.getName + ".vcf.gz")
- val sampleVcf = new File(outputDir, inputBam.getName + ".vcf.gz")
-
- //TODO: add proper class with piping support, see also issue #114
- add(new CommandLineFunction {
- @Input
- var input = inputBam
-
- @Output
- var output = sampleVcf
-
- def commandLine: String = mp.cmdPipe + " | " + bt.cmdPipeInput + " > " + output + " && tabix -p vcf " + output
- })
- sampleVcf
+ add(mp | bt)
+ bt.output
}
val cv = new CombineVariants(qscript)
@@ -238,10 +220,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
def addJobs() {
val rawFiles = inputBams.map(bamFile => {
+ val mp = new SamtoolsMpileup(qscript) {
+ override def configName = "samtoolsmpileup"
+ override def defaults = Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
+ }
+ mp.input :+= bamFile
+
val m2v = new MpileupToVcf(qscript)
m2v.inputBam = bamFile
m2v.output = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.vcf")
- add(m2v)
+ add(mp | m2v)
val vcfFilter = new VcfFilter(qscript) {
override def configName = "vcffilter"
--
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