Fixed issues with peak call generators.

chipathlon/module_generator.py

@@ -74,10 +74,11 @@ class ModuleGenerator(object):
         all_jobs = prev_results[0].all_jobs
         all_markers = final_result.all_markers
         results = []
-        for job_name in self.module.get_job_names(all_markers[self.module.name])[:-1]:
+        for job_dict in self.module.get_job_list(all_markers[self.module.name])[:-1]:
+            job_name = job_dict.keys()[0]
+            job_info = job_dict[job_name]
             all_jobs.append(self.workflow_jobs[job_name])
-            output_list = self.module.get_job_params(all_markers[self.module.name], job_name)["outputs"]
-            for output_info in output_list:
+            for output_info in job_info["outputs"]:
                 logical_name = output_info.keys()[0]
                 result = Result(logical_name, final_result.control_samples, final_result.signal_samples, all_markers, all_jobs, should_save=False)
                 results.append(result)

chipathlon/peak_call_generator.py

@@ -229,7 +229,7 @@ class PeakCallGenerator(ModuleGenerator):
             run.add_result("peak_call", result)
             self.call_pairs[result.full_name] = paired_result
 
-        return run.get_results("peak_call", "results_sorted.narrowPeak")
+        return run.get_results("peak_call", "results_sorted.bed")
 
     def find_prev_results(self, run, result):
         """

chipathlon/workflow_module.py

@@ -44,7 +44,7 @@ class WorkflowModule(object):
             pass
         return
 
-    def _get_job_list(self, markers):
+    def get_job_list(self, markers):
         """
         :param markers: A dictionary containing marker values for the module.
         :type markers: dict
@@ -119,7 +119,7 @@ class WorkflowModule(object):
                     # If the key is a job, we need to add the job for every
                     # possible marker depending on recursion depth.
                     for marker_values in itertools.product(*[marker[1] for marker in add_markers.iteritems()]):
-                        wlist = self._get_job_list(dict(zip(self.order, marker_values)))
+                        wlist = self.get_job_list(dict(zip(self.order, marker_values)))
                         wlist.append(item)
                 elif "[" in key and "]" in key:
                     # Split by either [ or ]
@@ -159,7 +159,7 @@ class WorkflowModule(object):
         return
 
     def get_job_params(self, markers, job_name):
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         for job_dict in job_list:
             if job_name == job_dict.keys()[0]:
                 return job_dict[job_name]
@@ -172,7 +172,7 @@ class WorkflowModule(object):
 
         Returns a list of job names that match the provided markers.
         """
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         job_names = []
         for job_dict in job_list:
             job_names.append(job_dict.keys()[0])
@@ -288,7 +288,7 @@ class WorkflowModule(object):
         inputs = []
         additional_inputs = []
         outputs = []
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         for job_dict in job_list:
             job_name = job_dict.keys()[0]
             job_info = job_dict[job_name]
@@ -323,7 +323,7 @@ class WorkflowModule(object):
 
         Walk through the jobs in the modules and add the jobs to the workflow.
         """
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         for job_dict in job_list:
             job_name = job_dict.keys()[0]
             job_info = job_dict[job_name]
@@ -352,7 +352,7 @@ class WorkflowModule(object):
 
     def get_dependent_jobs(self, dax, master_jobs, master_files, markers, inputs, additional_inputs, outputs):
         dep_list = []
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         for job_dict in job_list:
             job_name = job_dict.keys()[0]
             job_info = job_dict[job_name]
@@ -363,7 +363,7 @@ class WorkflowModule(object):
         return dep_list
 
     def get_final_outputs(self, markers):
-        job_list = self._get_job_list(markers)
+        job_list = self.get_job_list(markers)
         job_dict = job_list[-1]
         job_name = job_dict.keys()[0]
         outputs = job_dict[job_name]["outputs"]