Indent Job.Runner, add sanity checks

BD2KGenomics · Jun 28, 2016 · b812b86 · b812b86
1 parent 79e3542
commit b812b86
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/src/toil_scripts/batch_alignment/bwa_alignment.py b/src/toil_scripts/batch_alignment/bwa_alignment.py
@@ -285,9 +285,15 @@ def main():
             require(os.path.exists(args.manifest), '{} not found and no sample provided. '
                                                    'Please run "generate-manifest"'.format(args.manifest))
         # Parse config
-
-    # Launch Pipeline
-    Job.Runner.startToil(Job.wrapJobFn(download_shared_files, inputs, options.sample, options.output_dir), options)
+        parsed_config = {x.replace('-', '_'): y for x, y in yaml.load(open(args.config).read()).iteritems()}
+        config = argparse.Namespace(**parsed_config)
+        config.maxCores = int(args.maxCores) if args.maxCores else sys.maxint
+        samples = [args.sample] if args.sample else parse_manifest(args.manifest)
+        # Sanity checks
+        require(config.ref, 'Missing URL for reference file: {}'.format(config.ref))
+        require(config.output_dir, 'No output location specified: {}'.format(config.output_dir))
+        # Launch Pipeline
+        Job.Runner.startToil(Job.wrapJobFn(download_reference_files, config, samples), args)
 
 
 if __name__ == "__main__":