'make_fastqs': add support for Illumina indexes to 10x_multiome_gex' & '10x_multiome_atac' protocols.

Updates the Fastq generation pipeline to add support for the '10x_multiome_*' protocols to operate with sample sheets with Illumina index sequences (10x indexes are also still supported).

Author: pjbriggs

auto_process_ngs/bcl2fastq/pipeline.py

@@ -1018,6 +1018,9 @@ def _build_pipeline(self):
             elif pipeline_variant == "10x_cellranger-atac" and not has_10x_indexes:
                 # Switch to standard pipeline for 10x ATAC without 10x indexes
                 pipeline_variant = "standard"
+            elif pipeline_variant == "10x_cellranger-arc" and not has_10x_indexes:
+                # Switch to standard pipeline for 10x multiome without 10x indexes
+                pipeline_variant = "standard"
             self.report("- Pipeline variant: %s" % pipeline_variant)
 
             #########################

auto_process_ngs/bcl2fastq/protocols.py

@@ -130,12 +130,14 @@
         "description": "10x Genomics single cell multiome ATAC-seq data "
         "(pooled with GEX data)",
         "pipeline_variant": "10x_cellranger-arc",
-        "supported_indexes": ("10X",),
+        "supported_indexes": ("ILLUMINA", "10X",),
         "r1_length": 50,
         "r2_length": 24,
         "r3_length": 49,
         "i1_length": 8,
         "override_template": "RIRR",
+        "minimum_trimmed_read_length": 8,
+        "mask_short_adapter_reads": 8,
         "tenx_filter_single_index": True,
         "no_lane_splitting": False,
         "create_fastq_for_index_read": True,
@@ -153,11 +155,13 @@
         "description": "10x Genomics single cell multiome GEX data "
         "(pooled with ATAC data)",
         "pipeline_variant": "10x_cellranger-arc",
-        "supported_indexes": ("10X",),
+        "supported_indexes": ("ILLUMINA", "10X",),
         "r1_length": 28,
         "r2_length": 90,
         "i1_length": 10,
         "i2_length": 10,
+        "minimum_trimmed_read_length": 8,
+        "mask_short_adapter_reads": 8,
         "tenx_filter_dual_index": True,
         "no_lane_splitting": False,
         "create_fastq_for_index_read": True,