From 4a544d5308eddce56d474d199dbe9a29c1aef9e4 Mon Sep 17 00:00:00 2001
From: Peter Briggs <peter.briggs@manchester.ac.uk>
Date: Thu, 14 Dec 2023 11:11:36 +0000
Subject: [PATCH] qc/protocols: implement new protocol for 10x Cytassist Visium
 PEX data.

---
 auto_process_ngs/qc/protocols.py           | 19 ++++++++++++++++---
 auto_process_ngs/test/qc/test_protocols.py |  2 +-
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/auto_process_ngs/qc/protocols.py b/auto_process_ngs/qc/protocols.py
index 2e5bf3ea8..16c721335 100644
--- a/auto_process_ngs/qc/protocols.py
+++ b/auto_process_ngs/qc/protocols.py
@@ -259,7 +259,7 @@ class in the ``check_outputs`` method; new modules must be added
     },
 
     "10x_Visium_FFPE": {
-        "description": "10xGenomics Visium FFPE spatial data",
+        "description": "10xGenomics Visium FFPE spatial RNA-seq/GEX",
         "reads": {
             "seq_data": ('r2:1-50',),
             "index": ('r1',)
@@ -274,6 +274,18 @@ class in the ``check_outputs`` method; new modules must be added
         ]
     },
 
+    "10x_Visium_FFPE_PEX": {
+        "description": "10xGenomics Visium FFPE spatial PEX",
+        "reads": {
+            "seq_data": ('r2:1-50',),
+            "index": ('r1',)
+        },
+        "qc_modules": [
+            'fastqc',
+            'sequence_lengths'
+        ]
+    },
+
     "ParseEvercode": {
         "description": "Parse Biosciences Evercode data",
         "reads": {
@@ -635,9 +647,10 @@ def determine_qc_protocol(project):
                                              "10xGenomics CytAssist Visium"):
         # 10xGenomics Visium spatial transcriptomics
         if project.info.library_type in ("FFPE Spatial RNA-seq",
-                                         "FFPE Spatial GEX",
-                                         "FFPE Spatial PEX"):
+                                         "FFPE Spatial GEX"):
             protocol = "10x_Visium_FFPE"
+        elif project.info.library_type == "FFPE Spatial PEX":
+            protocol = "10x_Visium_FFPE_PEX"
         else:
             protocol = "10x_Visium"
     # Multiome ATAC+GEX
diff --git a/auto_process_ngs/test/qc/test_protocols.py b/auto_process_ngs/test/qc/test_protocols.py
index bf812b9a0..a1920d456 100644
--- a/auto_process_ngs/test/qc/test_protocols.py
+++ b/auto_process_ngs/test/qc/test_protocols.py
@@ -658,7 +658,7 @@ def test_determine_qc_protocol_10x_visium_cytassist_ffpe_pex(self):
         project = AnalysisProject("PJB",
                                   os.path.join(self.wd,"PJB"))
         self.assertEqual(determine_qc_protocol(project),
-                         "10x_Visium_FFPE")
+                         "10x_Visium_FFPE_PEX")
 
     def test_determine_qc_protocol_10x_multiome_atac(self):
         """determine_qc_protocol: single cell multiome ATAC run (10xGenomics Multiome ATAC)