Commit 8e8b825e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

make aln/sampe/samse jobs intermediate

parent bdc6999e
......@@ -30,7 +30,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument, ClassType }
import scala.math._
class Mapping(val root: Configurable) extends QScript with BiopetQScript {
qscript =>
def this() = this(null)
@Input(doc = "R1 fastq file", shortName = "R1", required = true)
......@@ -156,13 +155,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
val fastSplitter_R1 = new FastqSplitter(this)
fastSplitter_R1.input = fastq_R1
for ((chunkDir, fastqfile) <- chunks) fastSplitter_R1.output :+= fastqfile._1
add(fastSplitter_R1, isIntermediate = true)
fastSplitter_R1.isIntermediate = true
add(fastSplitter_R1)
if (paired) {
val fastSplitter_R2 = new FastqSplitter(this)
fastSplitter_R2.input = fastq_R2
for ((chunkDir, fastqfile) <- chunks) fastSplitter_R2.output :+= fastqfile._2
add(fastSplitter_R2, isIntermediate = true)
fastSplitter_R2.isIntermediate = true
add(fastSplitter_R2)
}
}
......@@ -219,12 +220,15 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaAlnR1.fastq = R1
bwaAlnR1.deps = deps
bwaAlnR1.output = swapExt(output.getParent, output, ".bam", ".R1.sai")
bwaAlnR1.isIntermediate = true
add(bwaAlnR1)
val samFile: File = if (paired) {
val bwaAlnR2 = new BwaMem(this)
val bwaAlnR2 = new BwaAln(this)
bwaAlnR2.fastq = R2
bwaAlnR2.deps = deps
bwaAlnR2.output = swapExt(output.getParent, output, ".bam", ".R2.sai")
bwaAlnR2.isIntermediate = true
add(bwaAlnR2)
val bwaSampe = new BwaSampe(this)
......@@ -234,6 +238,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaSampe.saiR2 = bwaAlnR2.output
bwaSampe.r = getReadGroup
bwaSampe.output = swapExt(output.getParent, output, ".bam", ".sam")
bwaSampe.isIntermediate = true
add(bwaSampe)
bwaSampe.output
......@@ -243,6 +248,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaSamse.sai = bwaAlnR1.output
bwaSamse.r = getReadGroup
bwaSamse.output = swapExt(output.getParent, output, ".bam", ".sam")
bwaSamse.isIntermediate = true
add(bwaSamse)
bwaSamse.output
......@@ -261,7 +267,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaCommand.deps = deps
bwaCommand.R = getReadGroup
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
add(bwaCommand, isIntermediate = true)
bwaCommand.isIntermediate = true
add(bwaCommand)
val sortSam = SortSam(this, bwaCommand.output, output)
if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
add(sortSam)
......@@ -287,7 +294,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
stampyCmd.readgroup = RG
stampyCmd.sanger = true
stampyCmd.output = this.swapExt(output.getParent, output, ".bam", ".sam")
add(stampyCmd, isIntermediate = true)
stampyCmd.isIntermediate = true
add(stampyCmd)
val sortSam = SortSam(this, stampyCmd.output, output)
if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
add(sortSam)
......@@ -300,7 +308,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (paired) bowtie.R2 = R2
bowtie.deps = deps
bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
add(bowtie, isIntermediate = true)
bowtie.isIntermediate = true
add(bowtie)
return addAddOrReplaceReadGroups(bowtie.output, output)
}
......
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