Commit 23abce49 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change name checkExecutable to preProcesExecutable

parent e5e03434
......@@ -57,7 +57,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* Set default output file, threads and vmem for current job
*/
override def freezeFieldValues() {
checkExecutable
preProcesExecutable
beforeGraph
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
......@@ -77,7 +77,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
protected[core] def checkExecutable {
protected[core] def preProcesExecutable {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
......@@ -119,7 +119,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
* executes checkExecutable method and fill job report
*/
final protected def preCmdInternal {
checkExecutable
preProcesExecutable
beforeCmd
......@@ -170,7 +170,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
/** Get version from cache otherwise execute the version command */
def getVersion: String = {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
checkExecutable
preProcesExecutable
if (!BiopetCommandLineFunctionTrait.versionCache.contains(executable))
BiopetCommandLineFunctionTrait.versionCache += executable -> getVersionInternal
return BiopetCommandLineFunctionTrait.versionCache(executable)
......
......@@ -71,7 +71,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
}
for (function <- functions) function match {
case f: BiopetCommandLineFunctionTrait => {
f.checkExecutable
f.preProcesExecutable
f.beforeGraph
f.commandLine
}
......
......@@ -49,7 +49,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 4
override def beforeGraph {
this.checkExecutable
this.preProcesExecutable
val fastqcDir = new File(executable).getParent
......
......@@ -29,7 +29,7 @@ class ConiferExport(val root: Configurable) extends Conifer {
var output: File = _
override def beforeGraph {
this.checkExecutable
this.preProcesExecutable
}
override def cmdLine = super.cmdLine +
......
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