Merge pull request #1095 from fls-bioinformatics-core/make_fastqs-10x-use-illumina-indexes

'make_fastqs': enable `10x_chromium_sc` and `10x_visium` Fastq generation protocols to use sample sheets with Illumina indexes

Author: pjbriggs

auto_process_ngs/bcl2fastq/pipeline.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 #     pipeliner.py: utilities for building simple pipelines of tasks
-#     Copyright (C) University of Manchester 2017-2023 Peter Briggs
+#     Copyright (C) University of Manchester 2017-2025 Peter Briggs
 #
 """
 Module providing utility classes and functions for building simple
@@ -1927,8 +1927,13 @@ def rank_tasks(self):
         # lists of the required task ids as values
         required = dict()
         for task_id in self.task_list():
-            required[task_id] = [t.id()
-                                 for t in self.get_task(task_id)[1]]
+            try:
+                required[task_id] = [t.id()
+                                     for t in self.get_task(task_id)[1]]
+            except KeyError as ex:
+                raise PipelineError(f"Error ranking tasks: task with ID "
+                                    f"'{task_id}' wasn't added to the "
+                                    f"pipeline?")
         # Rank the task ids
         ranks = list()
         while required:

auto_process_ngs/pipeliner.py

@@ -36,9 +36,9 @@ def test_makefastqs_10x_atac_protocol_120(self):
 Adapter,CTGTCTCTTATACACATCT
 
 [Data]
-Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
-smpl1,smpl1,,,A001,SI-NA-A1,10xGenomics,
-smpl2,smpl2,,,A005,SI-NA-B1,10xGenomics,
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+smpl1,smpl1,,,A001,SI-NA-A1,A001,SI-NA-A1,10xGenomics,
+smpl2,smpl2,,,A005,SI-NA-B1,A005,SI-NA-B1,10xGenomics,
 """
         sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
         with open(sample_sheet,'w') as fp:
@@ -137,9 +137,9 @@ def test_makefastqs_10x_atac_protocol_200(self):
 Adapter,CTGTCTCTTATACACATCT
 
 [Data]
-Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
-smpl1,smpl1,,,A001,SI-NA-A1,10xGenomics,
-smpl2,smpl2,,,A005,SI-NA-B1,10xGenomics,
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+smpl1,smpl1,,,A001,SI-NA-A1,A001,SI-NA-A1,10xGenomics,
+smpl2,smpl2,,,A005,SI-NA-B1,A005,SI-NA-B1,10xGenomics,
 """
         sample_sheet = os.path.join(self.wd,"SampleSheet.csv")
         with open(sample_sheet,'w') as fp: