Merge pull request #156 from Workflomics/update_snakemake_extension

Update snakemake extension

Author: eladrion

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.workflomics</groupId>
 	<artifactId>APE</artifactId>
-	<version>2.6.0</version>
+	<version>2.6.1</version>
 	<packaging>jar</packaging>
 	<name>org.workflomics:APE</name>
 	<description>APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.</description>

src/main/java/nl/uu/cs/ape/APE.java

@@ -728,12 +728,12 @@ public static boolean writeSnakemakeWorkflows(SolutionsList allSolutions, boolea
         APEUtils.timerStart(timerID, true);
 
         /* Removing the existing files from the file system. */
-        prepareOutputDirectory(snakemakeFolder, "snakefile");
+        prepareOutputDirectory(snakemakeFolder, "smk");
         log.debug("Generating Snakemake files.");
 
         allSolutions.getParallelStream().filter(solution -> solution.getIndex() < noSnakemakeFiles).forEach(solution -> {
             try {
-                String titleSnakefile = solution.getFileName() + "_snakefile";
+                String titleSnakefile = solution.getFileName() + ".smk";
                 File script = snakemakeFolder.resolve(titleSnakefile).toFile();
 
                 if (createPartialImplementations) {