From acba06d7a5b07341b01ca55b4aa83b0f5a053a8f Mon Sep 17 00:00:00 2001
From: hpratt <hpratt111@live.com>
Date: Fri, 15 May 2020 13:53:04 -0400
Subject: [PATCH] delete stats directory

---
 src/main/kotlin/step/rsemquant.kt | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/main/kotlin/step/rsemquant.kt b/src/main/kotlin/step/rsemquant.kt
index 9b94ca3..9acbb43 100755
--- a/src/main/kotlin/step/rsemquant.kt
+++ b/src/main/kotlin/step/rsemquant.kt
@@ -44,8 +44,10 @@ fun CmdRunner.runRSEMQuant(parameters: RSEMParameters)  {
             ${ if (parameters.pairedEnd) "--paired-end" else "" } \
             ${parameters.bam} \
             ${parameters.outputDirectory.resolve(parameters.index.getFileName().toString().split(".tar.gz")[0])} \
-            ${parameters.outputDirectory.resolve("${parameters.outputPrefix}")} && \
-        chmod -R 666 ${parameters.outputDirectory.resolve("${parameters.outputPrefix}.stat")}
+            ${parameters.outputDirectory.resolve("${parameters.outputPrefix}")}
     """)
 
+    // delete unnecessary stat directory
+    parameters.outputDirectory.resolve("${parameters.outputPrefix}.stat").toFile().deleteRecursively()
+
 }