qc/reporting: update reporting of 10x multiplexed '#reads/cell'.

Updates the values reported for 10x Genomics multiplexed samples for the number of reads per cell; this is now explicitly calculated from the read and cell numbers.

Author: pjbriggs

auto_process_ngs/qc/reporting.py

@@ -2433,13 +2433,18 @@ def get_10x_value(self,field,cellranger_data,metrics,web_summary,
                     # Not sure if this fallback is redundant?
                     value = metrics.median_reads_per_cell
             elif cellranger_data.mode == "multi":
-                # Default is median for Cellranger>=7
+                # Calculate from number of reads/number of cells
                 try:
-                    value = metrics.median_reads_per_cell
-                except (AttributeError,MissingMetricError):
-                    # Cellranger 8.0.0 doesn't output median
-                    # reads so fall back to mean
-                    value = metrics.mean_reads_per_cell
+                    value = int(metrics.reads_in_cells)/int(metrics.cells)
+                except (AttributeError, MissingMetricError):
+                    # Fallbacks
+                    # Default is median for Cellranger<=7
+                    try:
+                        value = metrics.median_reads_per_cell
+                    except (AttributeError, MissingMetricError):
+                        # Cellranger 8.0.0 doesn't output median
+                        # reads so fall back to mean
+                        value = metrics.mean_reads_per_cell
             try:
                 # Assume that reads per cell is an
                 # integer and trap if it isn't (e.g.