Commit 755c54b0 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-chunking' into 'develop'

Fix chunking

Chunking was broken in develop, this should fix it

See merge request !250
parents 98bc93d9 df83160f
......@@ -85,9 +85,11 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
this.freeze()
}
var threadsCorrection = 0
protected def combineResources(commands: List[CommandLineResources]): Unit = {
commands.foreach(_.setResources())
nCoresRequest = Some(commands.map(_.threads).sum)
nCoresRequest = Some(commands.map(_.threads).sum + threadsCorrection)
_coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
memoryLimit = Some(_coreMemory * threads)
......
......@@ -36,7 +36,7 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
/** Returns command to execute */
def cmdLine = required(executable) +
(if (inputAsStdin) "" else required(input)) +
(if (inputAsStdin) "" else repeat(input)) +
(if (outputAsStsout) "" else " > " + required(output))
}
......
......@@ -39,10 +39,10 @@ trait Configurable extends ImplicitConversions {
def defaults: Map[String, Any] = Map()
/** This method merge defaults from the root to it's own */
protected def internalDefaults: Map[String, Any] = {
protected[config] def internalDefaults: Map[String, Any] = {
(root != null, defaults.isEmpty) match {
case (true, true) => root.defaults
case (true, false) => ConfigUtils.mergeMaps(defaults, root.defaults)
case (true, true) => root.internalDefaults
case (true, false) => ConfigUtils.mergeMaps(defaults, root.internalDefaults)
case (false, true) => globalConfig.defaults
case (false, false) => ConfigUtils.mergeMaps(defaults, globalConfig.defaults)
}
......
......@@ -153,29 +153,31 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
else None
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, Option[File], List[File]) =
def runTrimClip(R1_in: File, outDir: File, chunk: String): (File, Option[File]) =
runTrimClip(R1_in, None, outDir, chunk)
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, outDir: File): (File, Option[File], List[File]) =
def runTrimClip(R1_in: File, outDir: File): (File, Option[File]) =
runTrimClip(R1_in, None, outDir, "")
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File): (File, Option[File], List[File]) =
def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File): (File, Option[File]) =
runTrimClip(R1_in, R2_in, outDir, "")
/** Adds all chunkable jobs of flexiprep */
def runTrimClip(R1_in: File, R2_in: Option[File], outDir: File, chunkarg: String): (File, Option[File], List[File]) = {
def runTrimClip(R1_in: File,
R2_in: Option[File],
outDir: File,
chunkarg: String): (File, Option[File]) = {
val chunk = if (chunkarg.isEmpty || chunkarg.endsWith("_")) chunkarg else chunkarg + "_"
var R1 = R1_in
var R2 = R2_in
def deps: List[File] = Nil
val qcCmdR1 = new QcCommand(this, fastqc_R1)
qcCmdR1.input = R1_in
qcCmdR1.read = "R1"
qcCmdR1.output = if (paired) new File(fastqR1Qc.getAbsolutePath.stripSuffix(".gz"))
qcCmdR1.output = if (paired) new File(outDir, fastqR1Qc.getName.stripSuffix(".gz"))
else fastqR1Qc
qcCmdR1.deps :+= fastqc_R1.output
qcCmdR1.isIntermediate = paired || !keepQcFastqFiles
......@@ -184,7 +186,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if (paired) {
val qcCmdR2 = new QcCommand(this, fastqc_R2)
qcCmdR2.input = R2_in.get
qcCmdR2.output = new File(fastqR2Qc.get.getAbsolutePath.stripSuffix(".gz"))
qcCmdR2.output = new File(outDir, fastqR2Qc.get.getName.stripSuffix(".gz"))
qcCmdR2.read = "R2"
addSummarizable(qcCmdR2, "qc_command_R2")
......@@ -195,8 +197,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.refFastq = R1_in
fqSync.inputFastq1 = qcCmdR1.output
fqSync.inputFastq2 = qcCmdR2.output
fqSync.outputFastq1 = fastqR1Qc
fqSync.outputFastq2 = fastqR2Qc.get
fqSync.outputFastq1 = new File(outDir, fastqR1Qc.getName)
fqSync.outputFastq2 = new File(outDir, fastqR2Qc.get.getName)
fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
val pipe = new BiopetFifoPipe(this, fqSync :: Nil) {
......@@ -242,7 +244,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
outputFiles += (chunk + "output_R1" -> R1)
if (paired) outputFiles += (chunk + "output_R2" -> R2.get)
(R1, R2, deps)
(R1, R2)
}
/** Adds last non chunkable jobs */
......@@ -251,8 +253,14 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
throw new IllegalStateException("R1 and R2 file number is not the same")
if (fastq_R1.length > 1) {
add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
val zcat = new Zcat(this)
zcat.input = fastq_R1
add(zcat | new Gzip(this) > fastqR1Qc)
if (paired) {
val zcat = new Zcat(this)
zcat.input = fastq_R2
add(zcat | new Gzip(this) > fastqR2Qc.get)
}
}
outputFiles += ("output_R1_gzip" -> fastqR1Qc)
......
......@@ -118,8 +118,6 @@ class GentrapTest extends TestNGSuite with Matchers {
val functions = gentrap.functions.groupBy(_.getClass)
val numSamples = sampleConfig("samples").size
functions(classOf[Gsnap]).size should be >= 1
if (expMeasures.contains("fragments_per_gene")) {
gentrap.functions
.collect { case x: HtseqCount => x.output.toString.endsWith(".fragments_per_gene") }.size shouldBe numSamples
......
......@@ -116,7 +116,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"skip_markduplicates" -> skipMarkduplicates,
"aligner" -> aligner,
"chunking" -> chunking,
"numberChunks" -> numberChunks.getOrElse(1)
"numberChunks" -> (if (chunking) numberChunks.getOrElse(1) else None)
) ++ (if (root == null) Map("reference" -> referenceSummary) else Map())
override def reportClass = {
......@@ -204,13 +204,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
for ((chunkDir, fastqfile) <- chunks) {
var R1 = fastqfile._1
var R2 = fastqfile._2
var deps: List[File] = Nil
if (!skipFlexiprep) {
val flexiout = flexiprep.runTrimClip(R1, R2, new File(chunkDir, "flexiprep"), chunkDir)
logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
deps = flexiout._3
fastq_R1_output :+= R1
R2.foreach(R2 => fastq_R2_output :+= R2)
}
......@@ -218,15 +216,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val outputBam = new File(chunkDir, outputName + ".bam")
bamFiles :+= outputBam
aligner match {
case "bwa-mem" => addBwaMem(R1, R2, outputBam, deps)
case "bwa-aln" => addBwaAln(R1, R2, outputBam, deps)
case "bowtie" => addBowtie(R1, R2, outputBam, deps)
case "gsnap" => addGsnap(R1, R2, outputBam, deps)
case "bwa-mem" => addBwaMem(R1, R2, outputBam)
case "bwa-aln" => addBwaAln(R1, R2, outputBam)
case "bowtie" => addBowtie(R1, R2, outputBam)
case "gsnap" => addGsnap(R1, R2, outputBam)
// TODO: make TopHat here accept multiple input files
case "tophat" => addTophat(R1, R2, outputBam, deps)
case "stampy" => addStampy(R1, R2, outputBam, deps)
case "star" => addStar(R1, R2, outputBam, deps)
case "star-2pass" => addStar2pass(R1, R2, outputBam, deps)
case "tophat" => addTophat(R1, R2, outputBam)
case "stampy" => addStampy(R1, R2, outputBam)
case "star" => addStar(R1, R2, outputBam)
case "star-2pass" => addStar2pass(R1, R2, outputBam)
case _ => throw new IllegalStateException("Option aligner: '" + aligner + "' is not valid")
}
if (chunking && numberChunks.getOrElse(1) > 1 && config("chunk_metrics", default = false))
......@@ -267,10 +265,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Add bwa aln jobs */
def addBwaAln(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addBwaAln(R1: File, R2: Option[File], output: File): File = {
val bwaAlnR1 = new BwaAln(this)
bwaAlnR1.fastq = R1
bwaAlnR1.deps = deps
bwaAlnR1.output = swapExt(output.getParent, output, ".bam", ".R1.sai")
bwaAlnR1.isIntermediate = true
add(bwaAlnR1)
......@@ -278,7 +275,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val samFile: File = if (paired) {
val bwaAlnR2 = new BwaAln(this)
bwaAlnR2.fastq = R2.get
bwaAlnR2.deps = deps
bwaAlnR2.output = swapExt(output.getParent, output, ".bam", ".R2.sai")
bwaAlnR2.isIntermediate = true
add(bwaAlnR2)
......@@ -313,41 +309,47 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Adds bwa mem jobs */
def addBwaMem(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addBwaMem(R1: File, R2: Option[File], output: File): File = {
val bwaCommand = new BwaMem(this)
bwaCommand.R1 = R1
if (paired) bwaCommand.R2 = R2.get
bwaCommand.deps = deps
bwaCommand.R = Some(getReadGroupBwa)
val sortSam = new SortSam(this)
sortSam.output = output
add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
val pipe = bwaCommand | sortSam
pipe.isIntermediate = chunking || !skipMarkduplicates
pipe.threadsCorrection = -1
add(pipe)
output
}
def addGsnap(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addGsnap(R1: File, R2: Option[File], output: File): File = {
val zcatR1 = extractIfNeeded(R1, output.getParentFile)
val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
val gsnapCommand = new Gsnap(this)
gsnapCommand.input = if (paired) List(R1, R2.get) else List(R1)
gsnapCommand.deps = deps
gsnapCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
gsnapCommand.isIntermediate = true
add(gsnapCommand)
gsnapCommand.input = if (paired) List(zcatR1._2, zcatR2.get._2) else List(zcatR1._2)
gsnapCommand.output = swapExt(output.getParentFile, output, ".bam", ".sam")
val reorderSam = new ReorderSam(this)
reorderSam.input = gsnapCommand.output
reorderSam.output = swapExt(output.getParent, output, ".sorted.bam", ".reordered.bam")
add(reorderSam)
addAddOrReplaceReadGroups(reorderSam.output, output)
reorderSam.output = swapExt(output.getParentFile, output, ".sorted.bam", ".reordered.bam")
val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
Some(gsnapCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
pipe.threadsCorrection = -1
zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
add(pipe)
ar._2
}
def addTophat(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addTophat(R1: File, R2: Option[File], output: File): File = {
// TODO: merge mapped and unmapped BAM ~ also dealing with validation errors in the unmapped BAM
val tophat = new Tophat(this)
tophat.R1 = tophat.R1 :+ R1
if (paired) tophat.R2 = tophat.R2 :+ R2.get
tophat.output_dir = new File(outputDir, "tophat_out")
tophat.deps = deps
// always output BAM
tophat.no_convert_bam = false
// and always keep input ordering
......@@ -381,10 +383,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
reorderSam.output = swapExt(output.getParent, output, ".merge.bam", ".reordered.bam")
add(reorderSam)
addAddOrReplaceReadGroups(reorderSam.output, output)
val ar = addAddOrReplaceReadGroups(reorderSam.output, output)
add(ar._1)
ar._2
}
/** Adds stampy jobs */
def addStampy(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addStampy(R1: File, R2: Option[File], output: File): File = {
var RG: String = "ID:" + readgroupId + ","
RG += "SM:" + sampleId.get + ","
......@@ -399,10 +403,9 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val stampyCmd = new Stampy(this)
stampyCmd.R1 = R1
if (paired) stampyCmd.R2 = R2.get
stampyCmd.deps = deps
stampyCmd.readgroup = RG
stampyCmd.sanger = true
stampyCmd.output = this.swapExt(output.getParent, output, ".bam", ".sam")
stampyCmd.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
stampyCmd.isIntermediate = true
add(stampyCmd)
val sortSam = SortSam(this, stampyCmd.output, output)
......@@ -412,33 +415,54 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
/** Adds bowtie jobs */
def addBowtie(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
def addBowtie(R1: File, R2: Option[File], output: File): File = {
val zcatR1 = extractIfNeeded(R1, output.getParentFile)
val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
zcatR1._1.foreach(add(_))
zcatR2.foreach(_._1.foreach(add(_)))
val bowtie = new Bowtie(this)
bowtie.R1 = R1
if (paired) bowtie.R2 = R2
bowtie.deps = deps
bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
bowtie.R1 = zcatR1._2
if (paired) bowtie.R2 = Some(zcatR2.get._2)
bowtie.output = this.swapExt(output.getParentFile, output, ".bam", ".sam")
bowtie.isIntermediate = true
add(bowtie)
addAddOrReplaceReadGroups(bowtie.output, output)
val ar = addAddOrReplaceReadGroups(bowtie.output, output)
val pipe = new BiopetFifoPipe(this, (Some(bowtie) :: Some(ar._1) :: Nil).flatten)
pipe.threadsCorrection = -1
add(pipe)
ar._2
}
/** Adds Star jobs */
def addStar(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
val starCommand = Star(this, R1, R2, outputDir, isIntermediate = true, deps = deps)
add(starCommand)
addAddOrReplaceReadGroups(starCommand.outputSam, output)
def addStar(R1: File, R2: Option[File], output: File): File = {
val zcatR1 = extractIfNeeded(R1, output.getParentFile)
val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
val starCommand = Star(this, zcatR1._2, zcatR2.map(_._2), outputDir, isIntermediate = true)
val ar = addAddOrReplaceReadGroups(starCommand.outputSam, output)
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
Some(starCommand) :: Some(ar._1) :: Nil).flatten)
pipe.threadsCorrection = -1
zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
add(pipe)
ar._2
}
/** Adds Start 2 pass jobs */
def addStar2pass(R1: File, R2: Option[File], output: File, deps: List[File]): File = {
val starCommand = Star._2pass(this, R1, R2, outputDir, isIntermediate = true, deps = deps)
def addStar2pass(R1: File, R2: Option[File], output: File): File = {
val zcatR1 = extractIfNeeded(R1, output.getParentFile)
val zcatR2 = if (paired) Some(extractIfNeeded(R2.get, output.getParentFile)) else None
zcatR1._1.foreach(add(_))
zcatR2.foreach(_._1.foreach(add(_)))
val starCommand = Star._2pass(this, zcatR1._2, zcatR2.map(_._2), outputDir, isIntermediate = true)
addAll(starCommand._2)
addAddOrReplaceReadGroups(starCommand._1, output)
val ar = addAddOrReplaceReadGroups(starCommand._1, output)
add(ar._1)
ar._2
}
/** Adds AddOrReplaceReadGroups */
def addAddOrReplaceReadGroups(input: File, output: File): File = {
def addAddOrReplaceReadGroups(input: File, output: File): (AddOrReplaceReadGroups, File) = {
val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, input, output)
addOrReplaceReadGroups.createIndex = true
......@@ -450,9 +474,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (readgroupSequencingCenter.isDefined) addOrReplaceReadGroups.RGCN = readgroupSequencingCenter.get
if (readgroupDescription.isDefined) addOrReplaceReadGroups.RGDS = readgroupDescription.get
if (!skipMarkduplicates) addOrReplaceReadGroups.isIntermediate = true
add(addOrReplaceReadGroups)
addOrReplaceReadGroups.output
(addOrReplaceReadGroups, addOrReplaceReadGroups.output)
}
/** Returns readgroup for bwa */
......@@ -477,22 +500,18 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
* @param runDir directory to extract when needed
* @return returns extracted file
*/
def extractIfNeeded(file: File, runDir: File): File = {
if (file == null) file
else if (file.getName.endsWith(".gz") || file.getName.endsWith(".gzip")) {
def extractIfNeeded(file: File, runDir: File): (Option[BiopetCommandLineFunction], File) = {
require(file != null)
if (file.getName.endsWith(".gz") || file.getName.endsWith(".gzip")) {
var newFile: File = swapExt(runDir, file, ".gz", "")
if (file.getName.endsWith(".gzip")) newFile = swapExt(runDir, file, ".gzip", "")
val zcatCommand = Zcat(this, file, newFile)
zcatCommand.isIntermediate = true
add(zcatCommand)
newFile
(Some(zcatCommand), newFile)
} else if (file.getName.endsWith(".bz2")) {
val newFile = swapExt(runDir, file, ".bz2", "")
val pbzip2 = Pbzip2(this, file, newFile)
pbzip2.isIntermediate = true
add(pbzip2)
newFile
} else file
(Some(pbzip2), newFile)
} else (None, file)
}
}
......
......@@ -91,28 +91,6 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)
//aligners
mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") if (paired) 2 else 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") if (paired) 1 else 0 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") if (paired) 0 else 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else if (aligner == "star-2pass") 3 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Bowtie]) shouldBe ((if (aligner == "bowtie") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Stampy]) shouldBe ((if (aligner == "stampy") 1 else 0) * chunks)
// Sort sam or replace readgroup
val sort = aligner match {
case "bwa-mem" | "bwa-aln" | "stampy" => "sortsam"
case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
}
if (aligner != "tophat") { // FIXME
//mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[AddOrReplaceReadGroups]) shouldBe ((if (sort == "replacereadgroups") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[MergeSamFiles]) shouldBe (if (skipMarkDuplicate && chunks > 1) 1 else 0)
mapping.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (if (skipMarkDuplicate) 0 else 1)
}
}
// remove temporary run directory all tests in the class have been run
......
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