Updated to recent changes in metapool

sequence_processing_pipeline/Pipeline.py

@@ -255,10 +255,6 @@ def __init__(self, configuration_file_path, run_id, input_file_path,
             # Optional lane_number parameter is ignored for Amplicon
             # runs, as the only valid value is 1.
         else:
-            # assume user_input_file_path references a sample-sheet.
-            self.sample_sheet = self._validate_sample_sheet(input_file_path)
-            self.mapping_file = None
-
             if lane_number is not None:
                 # confirm that the lane_number is a reasonable value.
                 lane_number = int(lane_number)
@@ -270,6 +266,10 @@ def __init__(self, configuration_file_path, run_id, input_file_path,
                 # with overwritten Lane number.
                 set_lane_number_in_sheet(input_file_path, lane_number)
 
+            # assume user_input_file_path references a sample-sheet.
+            self.sample_sheet = self._validate_sample_sheet(input_file_path)
+            self.mapping_file = None
+
         self._configure_profile()
 
     def get_software_configuration(self, software):

sequence_processing_pipeline/TellReadJob.py

@@ -16,8 +16,7 @@ class TellReadJob(Job):
     def __init__(self, run_dir, output_path, sample_sheet_path, queue_name,
                  node_count, wall_time_limit, jmem, modules_to_load,
                  qiita_job_id, label, reference_base,
-                 reference_map, tmp1_path, sing_script_path, lane,
-                 cores_per_task):
+                 reference_map, tmp1_path, sing_script_path, cores_per_task):
         """
         ConvertJob provides a convenient way to run bcl-convert or bcl2fastq
         on a directory BCL files to generate Fastq files.
@@ -61,6 +60,9 @@ def __init__(self, run_dir, output_path, sample_sheet_path, queue_name,
         self.sing_script_path = sing_script_path
         self.tmp1_path = tmp1_path
 
+        sheet = load_sample_sheet(self.sample_sheet_path)
+        lane = sheet.samples[0].Lane
+
         # force self.lane_number to be int. raise an Error if it's not.
         tmp = int(lane)
         if tmp < 1 or tmp > 8:

sequence_processing_pipeline/tests/test_TellReadJob.py

@@ -43,41 +43,13 @@ def setUp(self):
         self.cores_per_task = "4"
 
     def test_creation(self):
-        # confirm only sensible lane numbers are allowed.
-        with self.assertRaisesRegex(ValueError,
-                                    "'-1' is not a valid lane number"):
-            TellReadJob(self.run_dir, self.output_path, self.sample_sheet_path,
-                        self.queue_name, self.node_count, self.wall_time_limit,
-                        self.jmem, self.modules_to_load, self.qiita_job_id,
-                        self.label, self.reference_base, self.reference_map,
-                        self.tmp1_path, self.sing_script_path, -1,
-                        self.cores_per_task)
-
-        with self.assertRaisesRegex(ValueError,
-                                    "'0' is not a valid lane number"):
-            TellReadJob(self.run_dir, self.output_path, self.sample_sheet_path,
-                        self.queue_name, self.node_count, self.wall_time_limit,
-                        self.jmem, self.modules_to_load, self.qiita_job_id,
-                        self.label, self.reference_base, self.reference_map,
-                        self.tmp1_path, self.sing_script_path, 0,
-                        self.cores_per_task)
-
-        with self.assertRaisesRegex(ValueError,
-                                    "'9' is not a valid lane number"):
-            TellReadJob(self.run_dir, self.output_path, self.sample_sheet_path,
-                        self.queue_name, self.node_count, self.wall_time_limit,
-                        self.jmem, self.modules_to_load, self.qiita_job_id,
-                        self.label, self.reference_base, self.reference_map,
-                        self.tmp1_path, self.sing_script_path, 9,
-                        self.cores_per_task)
-
         # test basic good-path
         job = TellReadJob(self.run_dir, self.output_path,
                           self.sample_sheet_path, self.queue_name,
                           self.node_count, self.wall_time_limit,
                           self.jmem, self.modules_to_load, self.qiita_job_id,
                           self.label, self.reference_base, self.reference_map,
-                          self.tmp1_path, self.sing_script_path, self.lane,
+                          self.tmp1_path, self.sing_script_path,
                           self.cores_per_task)
 
         job._generate_job_script()