download job file instead of network mount

src/main/java/nl/munlock/App.java

@@ -29,8 +29,10 @@ public class App {
         // Make the irods connection
         Connection connection = new Connection(commandOptions);
 
-        // Downloading job files
-        Scanner scanner = new Scanner(new File(commandOptions.jobFile));
+        // Downloading job file
+        nl.munlock.irods.Generic.downloadFile(connection, new File(commandOptions.jobFile));
+
+        Scanner scanner = new Scanner(new File("." + commandOptions.jobFile));
         HashSet<String> hdts = new HashSet<>();
         HashSet<String> turtles = new HashSet<>();
         ArrayList<String> lines = new ArrayList<>();

src/test/java/AppTest.java

@@ -11,10 +11,10 @@ public class AppTest {
     @Test
     public void testPhyloseq() throws Exception {
         String[] args = {
-                "-i", "/Volumes/unlock-icat.irods.surfsara.nl/home/koehorst/phyloseq/MIB-Amplicon.job",
+                "-i", "/unlock/home/koehorst/phyloseq/TKI_BO3B.job",
                 "-database", "SILVA_138.1_SSURef_tax_silva.fasta.gz",
-                "-readLength", "70",
-                "-prefix", "MIB-AmpliconX"
+                "-readLength", "100",
+                "-prefix", "TKI_BO3B"
         };
         App.main(args);
     }