Commit 4e61e371 authored by Koehorst, Jasper's avatar Koehorst, Jasper
Browse files

improve messages

parent 18c597a9
Pipeline #14746 failed with stage
......@@ -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
......
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