improve messages

src/main/java/nl/munlock/yaml/NGTax.java

@@ -72,6 +72,12 @@ public class NGTax {
 
             IRODSFile destFile;
 
+            log.info("Read length set to " + commandOptions.read_len);
+//            if (commandOptions.read_len > 0) {
+//                workflow.for_read_len = commandOptions.read_len;
+//                workflow.rev_read_len = commandOptions.read_len;
+//            }
+
             if (files.size() == 0) {
                 log.warn("No files found");
             } else if (files.size() == 1) {
@@ -85,8 +91,9 @@ public class NGTax {
                     log.info("Obtaining read length information from RDF file");
                     workflow.setFor_read_len(Math.toIntExact(sequenceDataSet.getReadLength()));
                 } else if (commandOptions.read_len > 0) {
-                    if (commandOptions.read_len > sequenceDataSet.getReadLength())
+                    if (commandOptions.read_len > sequenceDataSet.getReadLength()) {
                         throw new Exception("Read length of " + commandOptions.read_len + " is larger than " + sequenceDataSet.getReadLength());
+                    }
                     log.info("Setting read length to " + commandOptions.read_len + " of " + sequenceDataSet.getReadLength());
                     workflow.setFor_read_len(Math.toIntExact(commandOptions.read_len));
                 } else {
@@ -115,6 +122,12 @@ public class NGTax {
                 } else {
                     log.error("RDF file does not contain read length information? Please provide read length information");
                 }
+            } else {
+                files.forEach(file -> {
+                    System.err.println(file.getFileName());
+                    System.err.println(file.getResource().getURI());
+                });
+                throw new Exception("More than 2 files detected...");
             }
 
             // Save to nl.wur.ssb.yaml format