Commit cd2a9aa4 authored by aknecht2's avatar aknecht2
Browse files

Cleaned up _check_grch38. Added handling for prefixes.

parent 241c210e
......@@ -182,13 +182,10 @@ class Workflow(object):
if not os.path.isfile(prefix + "." + ext) and not os.path.isfile(base_file + "." + ext):
missing.append(ext)
else:
fnew = File(gen_prefix + "." + ext)
if os.path.isfile(prefix + "." + ext):
fnew.addPFN(PFN(prefix + "." + ext, "local"))
else:
fnew.addPFN(PFN(base_file + "." + ext, "local"))
self.files[gen_prefix + "." + ext] = fnew
self.dax.addFile(fnew)
no_ext = os.path.isfile(prefix + "." + ext)
name = "%s.%s%s" % (gen_prefix, "" if no_ext else base_file_ext + ".", ext)
path = "%s.%s" % (prefix if no_ext else base_file, ext)
self._add_file(name, path, "local")
if len(missing) > 0:
self.err += "Genome defined with tool '%s' and assembly '%s' is missing additional_files with extensions %s.\n" % (run["align"], assembly, missing)
else:
......
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