Code review comments.

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNScoreVariants.java

@@ -27,6 +27,7 @@
 import java.util.concurrent.TimeUnit;
 import java.util.stream.StreamSupport;
 
+import static org.broadinstitute.hellbender.utils.io.Resource.LARGE_RUNTIME_RESOURCES_PATH;
 
 
 /**
@@ -176,8 +177,8 @@ public class CNNScoreVariants extends VariantWalker {
 
     private String scoreKey;
 
-    private static String resourcePathReadTensor = "large" + File.separator + "cnn_score_variants" + File.separator + "small_2d.json";
-    private static String resourcePathReferenceTensor = "large" + File.separator + "cnn_score_variants" + File.separator + "1d_cnn_mix_train_full_bn.json";
+    private static String resourcePathReadTensor = LARGE_RUNTIME_RESOURCES_PATH + "/cnn_score_variants/small_2d.json";
+    private static String resourcePathReferenceTensor = LARGE_RUNTIME_RESOURCES_PATH + "/cnn_score_variants/1d_cnn_mix_train_full_bn.json";
 
     @Override
     protected String[] customCommandLineValidation() {

src/main/java/org/broadinstitute/hellbender/utils/R/RScriptExecutor.java

@@ -93,7 +93,7 @@ public boolean exec() {
             if (!this.libraries.isEmpty()) {
                 List<String> tempLibraryPaths = new ArrayList<>();
                 for (RScriptLibrary library: this.libraries) {
-                    final File tempLibrary = library.writeLibrary(tempLibSourceDir);
+                    final File tempLibrary = library.writeLibraryToTempFile(tempLibSourceDir);
                     tempLibraryPaths.add(tempLibrary.getAbsolutePath());
                 }
 

src/main/java/org/broadinstitute/hellbender/utils/R/RScriptLibrary.java

@@ -36,13 +36,13 @@ public File writeTemp() {
     }
 
     /**
-     * Retrieve the resource for this library and write it to a File in {@code targetDir}. The File is not
-     * automatically scheduled for deletion and must be cleaned up by the caller.
+     * Retrieve the resource for this library and write it to a temp File in {@code targetDir}. The File is
+     * automatically scheduled for deletion on exit.
      * @param targetDir target directory where the File should be written
-     * @return the newly created File containing the library
+     * @return the newly created temporary File containing the library
      */
-    public File writeLibrary(final File targetDir) {
-        final File libraryFile = new File(targetDir, getLibraryName());
+    public File writeLibraryToTempFile(final File targetDir) {
+        final File libraryFile = IOUtils.createTempFileInDirectory(getLibraryName(), R_LIBRARY_SUFFIX, targetDir);
         // Note that the temporary filename generated by this ends with the resource path suffix containing
         // embedded digits: ".tar.dddddddddd.gz".
         IOUtils.writeResource(new Resource(getResourcePath(), RScriptLibrary.class), libraryFile);

src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java

@@ -402,13 +402,26 @@ public static PrintStream makePrintStreamMaybeGzipped(File file) throws IOExcept
      * @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
      */
     public static File createTempFile(String name, String extension) {
+        return createTempFileInDirectory(name, extension, null);
+    }
+
+    /**
+     * Creates a temp file in a target directory that will be deleted on exit
+     *
+     * This will also mark the corresponding Tribble/Tabix/BAM indices matching the temp file for deletion.
+     * @param name Prefix of the file.
+     * @param extension Extension to concat to the end of the file name.
+     * @param targetDir Directory in which to create the temp file. If null, the default temp directory is used.
+     * @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
+     */
+    public static File createTempFileInDirectory(final String name, String extension, final File targetDir) {
         try {
 
             if ( !extension.startsWith(".") ) {
                 extension = "." + extension;
             }
 
-            final File file = File.createTempFile(name, extension);
+            final File file = File.createTempFile(name, extension, targetDir);
             file.deleteOnExit();
 
             // Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file:
@@ -424,7 +437,6 @@ public static File createTempFile(String name, String extension) {
         }
     }
 
-
     /**
      * @param extension a file extension, may include 0 or more leading dots which will be replaced with a single dot
      * @return replace the final extension on a path with the given extension

src/main/java/org/broadinstitute/hellbender/utils/python/PythonScriptExecutor.java

@@ -117,7 +117,11 @@ public boolean executeScript(final Resource scriptResource, final List<String> p
         Utils.nonNull(scriptResource, "script resource cannot be null");
         // this File is automatically scheduled for deletion on exit
         final File tempResourceFile = IOUtils.writeTempResource(scriptResource);
-        return executeScript(tempResourceFile.getAbsolutePath(), pythonProcessArgs, scriptArgs);
+        try {
+            return executeScript(tempResourceFile.getAbsolutePath(), pythonProcessArgs, scriptArgs);
+        } finally {
+            FileUtils.deleteQuietly(tempResourceFile);
+        }
     }
 
     /**

src/test/java/org/broadinstitute/hellbender/utils/R/RScriptLibraryUnitTest.java

@@ -1,11 +1,12 @@
 package org.broadinstitute.hellbender.utils.R;
 
+import org.broadinstitute.hellbender.utils.test.BaseTest;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
 import java.io.File;
 
-public final class RScriptLibraryUnitTest {
+public final class RScriptLibraryUnitTest extends BaseTest {
     @Test(groups = {"R"})
     public void testProperties() {
         Assert.assertEquals(RScriptLibrary.GSALIB.getLibraryName(), "gsalib");
@@ -17,4 +18,15 @@ public void testWriteTemp() {
         final File file = RScriptLibrary.GSALIB.writeTemp();
         Assert.assertTrue(file.exists(), "R library was not written to temp file: " + file);
     }
+
+    @Test(groups = {"R"})
+    public void testWriteLibraryToTempFileInDir() {
+        final RScriptLibrary library = RScriptLibrary.GSALIB;
+        final File tempLibSourceDir = createTempDir("testWriteLibraryToTempFileInDir");
+        final File tempLibraryFile = library.writeLibraryToTempFile(tempLibSourceDir);
+        Assert.assertTrue(tempLibraryFile.exists(), "R library was not written to temp file: " + tempLibraryFile);
+        Assert.assertEquals(tempLibraryFile.getParentFile().getAbsolutePath(), (tempLibSourceDir.getAbsolutePath()),
+                "R library was not written to temp file: " + tempLibraryFile + " in dir: " + tempLibSourceDir);
+    }
+
 }

src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java

@@ -268,6 +268,15 @@ public void testWriteTempResourceFromPath(
         Assert.assertEquals(resourceContentsFirstLine, expectedFirstLine);
     }
 
+    @Test
+    public void testCreateTempFileInDirectory() {
+        final File tempDir = createTempDir("testCreateTempFileInDirectory");
+        final File tempFile = IOUtils.createTempFileInDirectory("testCreateTempFileInDirectory", ".txt", tempDir);
+        Assert.assertTrue(tempFile.exists(), "file was not written to temp file: " + tempFile);
+        Assert.assertEquals(tempFile.getParentFile().getAbsolutePath(), (tempDir.getAbsolutePath()),
+                "file was not written to temp file: " + tempFile + " in dir: " + tempDir);
+    }
+
     private String getFirstLineAndDeleteTempFile(final File tempResourceFile) throws IOException {
         String resourceContentsFirstLine = "";
         try (final FileReader fr = new FileReader(tempResourceFile);