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

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