'setup' command: also acquire and store 'run_configuration' metadata …

…item.

auto_process_ngs/commands/setup_cmd.py

@@ -14,6 +14,7 @@
 import shutil
 import logging
 from ..bcl2fastq.utils import get_bases_mask
+from ..bcl2fastq.utils import get_run_config
 from ..bcl2fastq.utils import get_sequencer_platform
 from ..bcl2fastq.utils import make_custom_sample_sheet
 from ..applications import general as general_applications
@@ -210,6 +211,8 @@ def setup(ap,data_dir,analysis_dir=None,sample_sheet=None,
         target = os.path.join(data_dir,"RunInfo.xml")
         run_info_xml = os.path.join(ap.tmp_dir,"RunInfo.xml")
         fetch_file(target,run_info_xml)
+        run_config = get_run_config(run_info_xml)
+        print("Run configuration: %s" % run_config)
         default_bases_mask = get_bases_mask(run_info_xml)
         print("Default bases mask: %s" % default_bases_mask)
     except Exception as ex:
@@ -225,6 +228,7 @@ def setup(ap,data_dir,analysis_dir=None,sample_sheet=None,
             raise Exception("Failed to acquire RunInfo.xml: %s" % ex)
         else:
             # Can ignore if Fastqs already exist
+            run_config = None
             default_bases_mask = None
     # Attempt to acquire RunParameters.xml
     try:
@@ -309,6 +313,7 @@ def setup(ap,data_dir,analysis_dir=None,sample_sheet=None,
     ap.metadata['instrument_run_number'] = instrument_run_number
     ap.metadata['instrument_flow_cell_id'] = flow_cell
     ap.metadata['flow_cell_mode'] = flow_cell_mode
+    ap.metadata['run_configuration'] = run_config
     ap.metadata['default_bases_mask'] = default_bases_mask
     ap.metadata['sequencer_model'] = model
     ap.metadata['source'] = data_source

auto_process_ngs/test/commands/test_setup_cmd.py

@@ -120,6 +120,8 @@ def test_autoprocess_setup(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
         # Delete to force write of data to disk
@@ -194,8 +196,10 @@ def test_autoprocess_setup_novaseq_run(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,"SP")
         self.assertEqual(ap.metadata.sequencer_model,"NovaSeq 5000")
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:76bp, I1:10bp, I2:10bp, R2:76bp")
         self.assertEqual(ap.metadata.default_bases_mask,
-                         "y76,I0,I10,y76")
+                         "y76,I10,I10,y76")
         # Delete to force write of data to disk
         del(ap)
         # Check directory exists
@@ -253,6 +257,8 @@ def test_autoprocess_setup_specify_facility_run_number(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
         # Delete to force write of data to disk
@@ -312,6 +318,8 @@ def test_autoprocess_setup_specify_analysis_number(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
         # Delete to force write of data to disk
@@ -369,6 +377,8 @@ def test_autoprocess_setup_non_canonical_run_name(self):
         self.assertEqual(ap.metadata.instrument_flow_cell_id,None)
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
 
@@ -537,6 +547,8 @@ def test_autoprocess_setup_external_samplesheet(self):
                          "AHGXXXX")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:76bp, I1:6bp, R2:76bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y76,I6,y76")
         # Delete to force write of data to disk
@@ -603,6 +615,8 @@ def test_autoprocess_setup_samplesheet_from_url(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
         # Delete to force write of data to disk
@@ -686,6 +700,8 @@ def test_autoprocess_setup_samplesheet_with_lanes(self):
                          "AHGXXXX")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:76bp, I1:6bp, R2:76bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y76,I6,y76")
         # Delete to force write of data to disk
@@ -772,6 +788,8 @@ def test_autoprocess_setup_samplesheet_with_lanes_and_trailing_lines(self):
                          "AHGXXXX")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:76bp, I1:6bp, R2:76bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y76,I6,y76")
         # Delete to force write of data to disk
@@ -839,6 +857,8 @@ def test_autoprocess_setup_import_extra_files(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")
         # Delete to force write of data to disk
@@ -916,6 +936,7 @@ def test_autoprocess_setup_from_casava_outputs(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,None)
         self.assertEqual(ap.metadata.default_bases_mask,None)
         # Delete to force write of data to disk
         del(ap)
@@ -997,6 +1018,7 @@ def test_autoprocess_setup_from_bcl2fastq2_outputs(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,None)
+        self.assertEqual(ap.metadata.run_configuration,None)
         self.assertEqual(ap.metadata.default_bases_mask,None)
         # Delete to force write of data to disk
         del(ap)
@@ -1111,5 +1133,7 @@ def test_autoprocess_setup_stores_sequencer_model(self):
                          "000000000-ABCDE1")
         self.assertEqual(ap.metadata.flow_cell_mode,None)
         self.assertEqual(ap.metadata.sequencer_model,"MiSeq")
+        self.assertEqual(ap.metadata.run_configuration,
+                         "R1:101bp, I1:8bp, I2:8bp, R2:101bp")
         self.assertEqual(ap.metadata.default_bases_mask,
                          "y101,I8,I8,y101")