Commit e42e39c6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix outputDirs

parent 1865f3b0
...@@ -48,7 +48,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -48,7 +48,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var f: String = "d" var f: String = "d"
@Argument(doc = "Output directory", required = true) @Argument(doc = "Output directory", required = true)
var w: String = _ var w: File = null
var noBfgs: Boolean = config("no_bfgs", default = false) var noBfgs: Boolean = config("no_bfgs", default = false)
...@@ -65,6 +65,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -65,6 +65,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var executableThreads: Option[String] = config("exe_pthreads") var executableThreads: Option[String] = config("exe_pthreads")
override def beforeGraph { override def beforeGraph {
require(w != null)
if (threads == 0) threads = getThreads(defaultThreads) if (threads == 0) threads = getThreads(defaultThreads)
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
super.beforeGraph super.beforeGraph
...@@ -73,24 +74,24 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -73,24 +74,24 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
case "d" if b.isEmpty => { case "d" if b.isEmpty => {
out +:= getBestTreeFile out +:= getBestTreeFile
for (t <- 0 until N.getOrElse(1)) { for (t <- 0 until N.getOrElse(1)) {
out +:= new File(w + File.separator + "RAxML_log." + n + ".RUN." + t) out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
out +:= new File(w + File.separator + "RAxML_parsimonyTree." + n + ".RUN." + t) out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
out +:= new File(w + File.separator + "RAxML_result." + n + ".RUN." + t) out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
} }
} }
case "d" if b.isDefined => out +:= getBootstrapFile case "d" if b.isDefined => out +:= getBootstrapFile
case "b" => { case "b" => {
out +:= new File(w + File.separator + "RAxML_bipartitionsBranchLabels." + n) out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
out +:= new File(w + File.separator + "RAxML_bipartitions." + n) out +:= new File(w, "RAxML_bipartitions." + n)
} }
case _ => case _ =>
} }
} }
def getBestTreeFile: File = new File(w + File.separator + "RAxML_bestTree." + n) def getBestTreeFile: File = new File(w, "RAxML_bestTree." + n)
def getBootstrapFile: File = new File(w + File.separator + "RAxML_bootstrap." + n) def getBootstrapFile: File = new File(w, "RAxML_bootstrap." + n)
def getBipartitionsFile: File = new File(w + File.separator + "RAxML_bipartitions." + n) def getBipartitionsFile: File = new File(w, "RAxML_bipartitions." + n)
def getInfoFile: File = new File(w + File.separator + "RAxML_info." + n) def getInfoFile: File = new File(w, "RAxML_info." + n)
def cmdLine = required(executable) + def cmdLine = required(executable) +
required("-m", m) + required("-m", m) +
...@@ -103,6 +104,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -103,6 +104,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
optional("-f", f) + optional("-f", f) +
optional("-t", t) + optional("-t", t) +
optional("-z", z) + optional("-z", z) +
conditional(noBfgs, "--no-bgfs") + conditional(noBfgs, "--no-bfgs") +
required("-T", threads) required("-T", threads)
} }
...@@ -33,7 +33,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -33,7 +33,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var outputFiles: List[File] = Nil var outputFiles: List[File] = Nil
@Argument(required = true) @Argument(required = true)
var outputDirectory: String = _ var outputDirectory: File = null
executable = config("exe", default = "run_gubbins.py") executable = config("exe", default = "run_gubbins.py")
var outgroup: Option[String] = config("outgroup") var outgroup: Option[String] = config("outgroup")
...@@ -49,7 +49,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -49,7 +49,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
override def beforeGraph: Unit = { override def beforeGraph: Unit = {
super.beforeGraph super.beforeGraph
jobLocalDir = new File(outputDirectory) require(outputDirectory != null)
jobLocalDir = outputDirectory
if (prefix.isEmpty) prefix = Some(fastafile.getName) if (prefix.isEmpty) prefix = Some(fastafile.getName)
val out: List[String] = List(".recombination_predictions.embl", val out: List[String] = List(".recombination_predictions.embl",
".recombination_predictions.gff", ".recombination_predictions.gff",
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment