Commit 8e796c00 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Move log file output work dir

parent 542c87f0
...@@ -38,17 +38,16 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit ...@@ -38,17 +38,16 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
@Input(doc = "Reference") @Input(doc = "Reference")
var reference: File = _ var reference: File = _
protected def cleverOutputDir: File = new File(cleverWorkDir, "work")
var cleverWorkDir: File = _ var cleverWorkDir: File = _
@Output(doc = "Clever VCF output") @Output(doc = "Clever VCF output")
lazy val outputvcf: File = { lazy val outputvcf: File = {
new File(cleverOutputDir, "predictions.vcf") new File(cleverWorkDir, "predictions.vcf")
} }
@Output(doc = "Clever raw output") @Output(doc = "Clever raw output")
lazy val outputraw: File = { lazy val outputraw: File = {
new File(cleverOutputDir, "predictions.raw.txt") new File(cleverWorkDir, "predictions.raw.txt")
} }
// var T: Option[Int] = config("T", default = defaultThreads) // var T: Option[Int] = config("T", default = defaultThreads)
...@@ -60,13 +59,13 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit ...@@ -60,13 +59,13 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
override def beforeGraph() { override def beforeGraph() {
super.beforeGraph() super.beforeGraph()
if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined") if (cleverWorkDir == null) throw new Exception("Clever :: Workdirectory is not defined")
if (reference == null) reference = referenceFasta() if (reference == null) reference = referenceFasta()
} }
def cmdLine = required(executable) + def cmdLine = required(executable) +
" --sorted " + required("--sorted") +
" --use_xa " + required("--use_xa") +
optional("-T", threads) + optional("-T", threads) +
conditional(f, "-f") + conditional(f, "-f") +
conditional(a, "-a") + conditional(a, "-a") +
...@@ -74,7 +73,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit ...@@ -74,7 +73,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
conditional(r, "-r") + conditional(r, "-r") +
required(input) + required(input) +
required(reference) + required(reference) +
required(cleverOutputDir) required(cleverWorkDir)
} }
object CleverCaller { object CleverCaller {
......
...@@ -23,10 +23,10 @@ class Clever(val root: Configurable) extends SvCaller { ...@@ -23,10 +23,10 @@ class Clever(val root: Configurable) extends SvCaller {
def name = "clever" def name = "clever"
def biopetScript() { def biopetScript() {
//TODO: check double directories
for ((sample, bamFile) <- inputBams) { for ((sample, bamFile) <- inputBams) {
val cleverDir = new File(outputDir, sample) val cleverDir = new File(outputDir, sample)
val clever = CleverCaller(this, bamFile, cleverDir) val clever = CleverCaller(this, bamFile, new File(cleverDir, "clever_output"))
clever.jobOutputFile = new File(cleverDir, ".CleverCaller.out")
add(clever) add(clever)
val cleverVCF = new CleverFixVCF(this) val cleverVCF = new CleverFixVCF(this)
......
Markdown is supported
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