Fail fast if index basename not found.

bigdatagenomics · Aug 26, 2019 · affd146 · affd146
1 parent 72ab229
commit affd146
Showing 1 changed file with 11 additions and 0 deletions.
diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala b/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala
@@ -17,6 +17,7 @@
  */
 package org.bdgenomics.cannoli
 
+import java.io.FileNotFoundException
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.fragment.{ FragmentDataset, InterleavedFASTQInFormatter }
@@ -67,6 +68,16 @@ class Bowtie2(
 
   override def apply(fragments: FragmentDataset): AlignmentRecordDataset = {
 
+    // fail fast if index basename not found
+    try {
+      absolute(args.indexPath)
+    } catch {
+      case e: FileNotFoundException => {
+        error("Basename of the index %s not found, touch an empty file at this path if it does not exist".format(args.indexPath))
+        throw e
+      }
+    }
+
     val builder = CommandBuilders.create(args.useDocker, args.useSingularity)
       .setExecutable(args.executable)
       .add("-x")