Commit 4d46a85e authored by Wai Yi Leung's avatar Wai Yi Leung

Update code to v0.4 branch and fix usage of Ln and memory settings of VMEM,...

Update code to v0.4 branch and fix usage of Ln and memory settings of VMEM, settings for memory will be committed to the shark-config branch with recommended defaults.
parent e306aa3e
......@@ -9,7 +9,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false)
override val defaultVmem = "6G"
override val defaultThreads = 1 // breakdancer can only work on 1 single thread
override val versionRegex = """.*[Vv]ersion:? (.*)""".r
......
......@@ -11,7 +11,6 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
private lazy val versionexecutable: File = config("version_exe", default = (new File(executable).getParent + "/ctk-version"))
override val defaultVmem = "4G"
override val defaultThreads = 8
override def versionCommand = versionexecutable.getAbsolutePath
......
......@@ -89,11 +89,12 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript {
variants.outputFile = this.outputvcf
// add the job
add(variants)
this.outputvcf
} else {
// TODO: pretify this
val ln = Ln(this, vcfFiles.head._2, this.outputvcf, relative = true)
add(ln)
ln.out
ln.output
}
outputFiles += ("vcf" -> this.outputvcf)
......
......@@ -12,7 +12,6 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
private lazy val versionexecutable: File = new File(executable)
override val defaultVmem = "8G"
override val defaultThreads = 1
override def versionCommand = versionexecutable.getAbsolutePath
......
......@@ -85,7 +85,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
alignmentDir + sampleId + ".merged.bam", true)
alignmentlink.isIntermediate = true
add(alignmentlink)
alignmentlink.out
alignmentlink.output
} else if (libraryBamfiles.size > 1) {
val mergeSamFiles = new SambambaMerge(qscript)
mergeSamFiles.input = libraryBamfiles
......
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