'make_fastqs': update tests now '10x_chromium_sc' can accept Illumina indexes.

Author: pjbriggs

auto_process_ngs/test/commands/test_make_fastqs_cmd.py

@@ -289,42 +289,6 @@ def test_make_fastqs_standard_protocol_specify_id(self):
                 os.path.join(analysis_dir,filen)),
                             "Missing file: %s" % filen)
 
-    #@unittest.skip("Skipped")
-    def test_make_fastqs_standard_protocol_exception_for_chromium_sc_indices(self):
-        """make_fastqs: standard protocol with Chromium SC indices raises exception
-        """
-        # Sample sheet with 10xGenomics Chromium SC indices
-        samplesheet_chromium_sc_indices = """[Data]
-Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
-smpl1,smpl1,,,A001,SI-GA-A1,10xGenomics,
-smpl2,smpl2,,,A005,SI-GA-B1,10xGenomics,
-smpl3,smpl3,,,A006,SI-GA-C1,10xGenomics,
-smpl4,smpl4,,,A007,SI-GA-D1,10xGenomics,
-"""
-        sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
-        with open(sample_sheet,'w') as fp:
-            fp.write(samplesheet_chromium_sc_indices)
-        # Create mock source data
-        illumina_run = MockIlluminaRun(
-            "171020_NB500968_00002_AHGXXXX",
-            "nextseq",
-            top_dir=self.wd)
-        illumina_run.create()
-        # Create mock bcl2fastq
-        MockBcl2fastq2Exe.create(os.path.join(self.bin,"bcl2fastq"))
-        os.environ['PATH'] = "%s:%s" % (self.bin,
-                                        os.environ['PATH'])
-        # Do the test
-        ap = AutoProcess(settings=self.settings)
-        ap.setup(os.path.join(self.wd,
-                              "171020_NB500968_00002_AHGXXXX"),
-                 sample_sheet=sample_sheet)
-        self.assertTrue(ap.params.sample_sheet is not None)
-        self.assertRaises(Exception,
-                          make_fastqs,
-                          ap,
-                          protocol="standard")
-
     #@unittest.skip("Skipped")
     def test_make_fastqs_standard_protocol_stores_bases_mask(self):
         """make_fastqs: standard protocol stores supplied bases mask