Commit 9ce0cde0 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Order fixes

parent 06ea4025
......@@ -56,7 +56,7 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
@Argument(doc = "Work directory")
var outputPrefix: File = _
@Output(doc = "Output file of pindel, pointing to the DEL file")
@Output(doc = "Output file of Pindel, pointing to the DEL file")
var outputFile: File = _
@Output(doc = "", required = false)
......@@ -159,7 +159,6 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
}
// set the output file, the DELetion call is always made
// TODO: add more outputs for the LI, SI, INV etc...
outputFile = new File(outputPrefix + File.separator, "sample_D")
}
......
......@@ -57,6 +57,7 @@ class Pindel(val root: Configurable) extends SvCaller {
val todayformat = new SimpleDateFormat("yyyyMMdd")
val pindelVcf = new PindelVCF(this)
pindelVcf.deps ::= pindel.outputFile
pindelVcf.pindelOutputInputHolder = pindel.outputFile
pindelVcf.pindelOutputRoot = Some(new File(pindelDir, "sample"))
pindelVcf.rDate = todayformat.format(today) // officially, we should enter the date of the genome here
......
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