Commit 553d7899 authored by aknecht2's avatar aknecht2
Browse files

Fixed typos in workflow & workflow_module. Fixed single-end read handling.

parent cf52cf6d
......@@ -262,7 +262,7 @@ class Workflow(object):
if len(experiment_data) < len(control_base):
control_data = [random.choice(control_base) for i in range(0, len(experiment_data))]
elif len(experiment_data) > len(control_base):
control_data = random.shuffle(control_base) + [random.choice(control_base) for i in range(0, len(experiment_data) - len(control_base))]
control_data = control_base + [random.choice(control_base) for i in range(0, len(experiment_data) - len(control_base))]
else:
control_data = control_base
random.shuffle(control_data)
......@@ -298,7 +298,7 @@ class Workflow(object):
self.modules["align"].add_jobs(self.dax, self.jobs, self.files, prefix, markers, input_files, additional_files)
else:
markers["read_end"] = "single"
prefix = "%s_%s" % (run["experiment"], f["accession"])
prefix = "%s_%s" % (run["experiment"], file_tuple[0]["accession"])
input_files["download_1.fastq"] = "%s.fastq.gz" % (prefix,)
self.modules["align"].add_jobs(self.dax, self.jobs, self.files, prefix, markers, input_files, additional_files)
return
......
......@@ -127,7 +127,7 @@ class WorkflowModule(object):
for file_id in job_info[file_type]:
if file_id not in file_list and file_id not in output_files:
if prefix is None or self._get_full_name(prefix, markers, file_id) in master_files:
file_list.append(f)
file_list.append(file_id)
return (input_files, additional_files, output_files)
def get_files(self, markers, prefix = None, master_files = {}):
......
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