From 15d58d5ba412278822e1dffe97a6dc399c7c8d0a Mon Sep 17 00:00:00 2001
From: Peter Briggs <peter.briggs@manchester.ac.uk>
Date: Mon, 4 Nov 2024 13:04:24 +0000
Subject: [PATCH] 'report' command: update reporting of multiplexed samples to
 handle multiple configs.

---
 auto_process_ngs/commands/report_cmd.py       | 20 +++---
 .../test/commands/test_report_cmd.py          | 65 +++++++++++++++++++
 2 files changed, 75 insertions(+), 10 deletions(-)

diff --git a/auto_process_ngs/commands/report_cmd.py b/auto_process_ngs/commands/report_cmd.py
index a854b23c6..a224a869b 100644
--- a/auto_process_ngs/commands/report_cmd.py
+++ b/auto_process_ngs/commands/report_cmd.py
@@ -741,16 +741,16 @@ def get_multiplexed_samples(project):
     if project.info.library_type in ("CellPlex",
                                      "CellPlex scRNA-seq",
                                      "Flex"):
-        # Fetch implicit multiplexed sample info from config
-        try:
-            multi_config = CellrangerMultiConfigCsv(
-                os.path.join(project.dirn,"10x_multi_config.csv"))
-            # Return multiplexed sample names
-            return multi_config.sample_names
-        except FileNotFoundError:
-            # Multiplexed samples expected but can't be identified
-            # Return empty list
-            return []
+        # Fetch implicit multiplexed sample info from configs
+        multiplexed_samples = []
+        for f in os.listdir(project.dirn):
+            if f.startswith("10x_multi_config.") and \
+               f.endswith(".csv"):
+                multi_config = CellrangerMultiConfigCsv(
+                    os.path.join(project.dirn, f))
+                multiplexed_samples.extend(multi_config.sample_names)
+        # Return multiplexed sample names
+        return sorted(multiplexed_samples)
     else:
         # No multiplexed samples expected
         # Return None
diff --git a/auto_process_ngs/test/commands/test_report_cmd.py b/auto_process_ngs/test/commands/test_report_cmd.py
index b5ef86b7e..7b0299816 100644
--- a/auto_process_ngs/test/commands/test_report_cmd.py
+++ b/auto_process_ngs/test/commands/test_report_cmd.py
@@ -2508,6 +2508,71 @@ def test_get_multiplexed_samples_10x_multi_config(self):
 ABM2,CMO302,ABM2
 ABM3,CMO303,ABM3
 ABM4,CMO304,ABM4
+""" % (fastq_dir,fastq_dir))
+        project = AnalysisProject(os.path.join(mockdir.dirn,'AB'))
+        self.assertEqual(get_multiplexed_samples(project),
+                         ["ABM1", "ABM2", "ABM3", "ABM4"])
+
+    def test_get_multiplexed_samples_multiple_10x_multi_configs(self):
+        """
+        report: test 'get_multiplexed_samples' (multiple 10x multi configs)
+        """
+        mockdir = MockAnalysisDirFactory.bcl2fastq2(
+            '170901_M00879_0087_000000000-AGEW9',
+            'miseq',
+            metadata={ "source": "testing",
+                       "run_number": 87,
+                       "sequencer_model": "MiSeq",
+                       "analysis_number": 2 },
+            project_metadata={
+                "AB": { "User": "Alison Bell",
+                        "Library type": "CellPlex scRNA-seq",
+                        "Organism": "Human",
+                        "PI": "Audrey Bower",
+                        "Single cell platform": "10xGenomics Chromium 3'v3",
+                        "Number of cells": None,
+                        "Sequencer model": "MiSeq" }
+            },
+            top_dir=self.dirn)
+        mockdir.create()
+        # Add cellranger multi config.csv files
+        with open(os.path.join(mockdir.dirn,
+                               "AB",
+                               "10x_multi_config.AB1.csv"),'wt') as fp:
+            fastq_dir = os.path.join(mockdir.dirn,
+                                     "AB",
+                                     "fastqs")
+            fp.write("""[gene-expression]
+reference,/data/refdata-cellranger-gex-GRCh38-2020-A
+
+[libraries]
+fastq_id,fastqs,lanes,physical_library_id,feature_types,subsample_rate
+AB1,%s,any,AB1,gene expression,
+AB1,%s,any,AB1,Multiplexing Capture,
+
+[samples]
+sample_id,cmo_ids,description
+ABM1,CMO301,ABM1
+ABM2,CMO302,ABM2
+""" % (fastq_dir,fastq_dir))
+        with open(os.path.join(mockdir.dirn,
+                               "AB",
+                               "10x_multi_config.AB2.csv"),'wt') as fp:
+            fastq_dir = os.path.join(mockdir.dirn,
+                                     "AB",
+                                     "fastqs")
+            fp.write("""[gene-expression]
+reference,/data/refdata-cellranger-gex-GRCh38-2020-A
+
+[libraries]
+fastq_id,fastqs,lanes,physical_library_id,feature_types,subsample_rate
+AB2,%s,any,AB2,gene expression,
+AB2,%s,any,AB2,Multiplexing Capture,
+
+[samples]
+sample_id,cmo_ids,description
+ABM3,CMO303,ABM3
+ABM4,CMO304,ABM4
 """ % (fastq_dir,fastq_dir))
         project = AnalysisProject(os.path.join(mockdir.dirn,'AB'))
         self.assertEqual(get_multiplexed_samples(project),