Commit 599cce86 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

picrust2 cwl workflow

parent c6c57a5f
Pipeline #27335 failed with stage
in 32 seconds
......@@ -48,7 +48,7 @@ public class Yaml {
log.info("Obtained " + assays.size() + " assays");
CommandOptionsQuality commandOptionsQuality = new CommandOptionsQuality(args);
FASTQC.generateQualityWorkflow(commandOptionsQuality, connection, assays);
} else if (commandOptions.cwl.matches("workflow_ngtax.cwl")) {
} else if (commandOptions.cwl.matches("workflow_ngtax.cwl") || commandOptions.cwl.matches("workflow_ngtax_picrust2.cwl")) {
log.info("Running ngtax analysis");
File domainDirectory = Files.createTempDir();
Domain domain = new Domain("file://"+domainDirectory);
......
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