Commit 42b34355 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing dir names

parent 7d530c20
...@@ -104,7 +104,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -104,7 +104,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
case _ => case _ =>
} }
val logDir = new File(outputDir, ".log" + File.separator + BiopetQCommandLine.timestamp) val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite)) if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
globalConfig.writeReport(new File(logDir, "config")) globalConfig.writeReport(new File(logDir, "config"))
......
...@@ -77,7 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi ...@@ -77,7 +77,7 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
val pipelineConfig = globalConfig.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]] val pipelineConfig = globalConfig.map.getOrElse(pipelineName, Map()).asInstanceOf[Map[String, Any]]
val pipelineOutputDir = new File(globalConfig.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString) val pipelineOutputDir = new File(globalConfig.map.getOrElse("output_dir", pipelineConfig.getOrElse("output_dir", "./")).toString)
BiopetQScript.checkOutputDir(pipelineOutputDir) BiopetQScript.checkOutputDir(pipelineOutputDir)
val logDir: File = new File(pipelineOutputDir, ".log" + File.separator + BiopetQCommandLine.timestamp) val logDir: File = new File(pipelineOutputDir, ".log" + File.separator + pipelineName + "." + BiopetQCommandLine.timestamp)
logDir.mkdirs() logDir.mkdirs()
val logFile = new File(logDir, "biopet.log") val logFile = new File(logDir, "biopet.log")
......
...@@ -50,6 +50,7 @@ object WriteDependencies extends Logging with Configurable { ...@@ -50,6 +50,7 @@ object WriteDependencies extends Logging with Configurable {
* @param outputDir * @param outputDir
*/ */
def writeDependencies(functions: Seq[QFunction], outputDir: File): Unit = { def writeDependencies(functions: Seq[QFunction], outputDir: File): Unit = {
outputDir.mkdirs()
logger.info("Start calculating dependencies") logger.info("Start calculating dependencies")
val errorOnMissingInput: Boolean = config("error_on_missing_input", false) val errorOnMissingInput: Boolean = config("error_on_missing_input", false)
......
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