tenx/utils: update 'make_multi_config_template' for Cellranger 9.0.0.

auto_process_ngs/tenx/utils.py

@@ -568,6 +568,13 @@ def make_multi_config_template(f,reference=None,probe_set=None,
         cellranger_version = DEFAULT_CELLRANGER_VERSION
     else:
         cellranger_version = str(cellranger_version)
+    # Major version
+    try:
+        cellranger_major_version = int(cellranger_version.split(".")[0])
+    except Exception as ex:
+        raise Exception(f"'{cellranger_version}': unable to extract "
+                        f"Cellranger major  version from version string: "
+                        f"{ex}")
     # Normalise and check supplied library type
     if library_type.startswith("CellPlex"):
         library_type = "cellplex"
@@ -605,14 +612,14 @@ def make_multi_config_template(f,reference=None,probe_set=None,
                      (probe_set if probe_set
                       else "/path/to/probe/set"))
         fp.write("#force-cells,n\n")
-        if cellranger_version.startswith("7."):
+        if cellranger_major_version == 7:
             # Cellranger 7.* targetted
             if no_bam is not None:
                 fp.write("no-bam,%s\n" % str(no_bam).lower())
             else:
                 fp.write("#no-bam,true|false\n")
-        elif cellranger_version.startswith("8."):
-            # Cellranger 8.* targetted
+        elif cellranger_major_version in (8, 9):
+            # Cellranger 8.* or 9.* targetted
             if no_bam is not None:
                 fp.write("create-bam,%s\n" % str(not no_bam).lower())
             else:

auto_process_ngs/test/tenx/test_utils.py

@@ -789,6 +789,41 @@ def test_make_multi_config_template_cellplex_scrnaseq_800(self):
                                         if not line.startswith('##')])
         self.assertEqual(expected_content,actual_content)
 
+    def test_make_multi_config_template_cellplex_900(self):
+        """
+        make_multi_config_template: check CellPlex template (9.0.0)
+        """
+        expected_content = """[gene-expression]
+reference,/data/mm10_transcriptome
+#force-cells,n
+create-bam,true
+#cmo-set,/path/to/custom/cmo/reference
+
+#[feature]
+#reference,/path/to/feature/reference
+
+[libraries]
+fastq_id,fastqs,lanes,physical_library_id,feature_types,subsample_rate
+PJB_CML,/runs/novaseq_50/fastqs,any,PJB_CML,[Gene Expression|Multiplexing Capture],
+PJB_GEX,/runs/novaseq_50/fastqs,any,PJB_GEX,[Gene Expression|Multiplexing Capture],
+
+[samples]
+sample_id,cmo_ids,description
+MULTIPLEXED_SAMPLE,CMO1|CMO2|...,DESCRIPTION
+"""
+        out_file = os.path.join(self.wd,"10x_multi_config.csv")
+        make_multi_config_template(out_file,
+                                   reference="/data/mm10_transcriptome",
+                                   fastq_dir="/runs/novaseq_50/fastqs",
+                                   samples=("PJB_CML","PJB_GEX"),
+                                   library_type="CellPlex",
+                                   cellranger_version="9.0.0")
+        self.assertTrue(os.path.exists(out_file))
+        with open(out_file,'rt') as fp:
+            actual_content = '\n'.join([line for line in fp.read().split('\n')
+                                        if not line.startswith('##')])
+        self.assertEqual(expected_content,actual_content)
+
     def test_make_multi_config_template_flex_700(self):
         """
         make_multi_config_template: check Flex template (7.1.0)
@@ -863,6 +898,43 @@ def test_make_multi_config_template_flex_800(self):
                                         if not line.startswith('##')])
         self.assertEqual(expected_content,actual_content)
 
+    def test_make_multi_config_template_flex_900(self):
+        """
+        make_multi_config_template: check Flex template (9.0.0)
+        """
+        expected_content = """[gene-expression]
+reference,/data/mm10_transcriptome
+probe-set,/data/mm10_probe_set.csv
+#force-cells,n
+create-bam,false
+#cmo-set,/path/to/custom/cmo/reference
+
+#[feature]
+#reference,/path/to/feature/reference
+
+[libraries]
+fastq_id,fastqs,lanes,physical_library_id,feature_types,subsample_rate
+PJB_Flex,/runs/novaseq_50/fastqs,any,PJB_Flex,[Gene Expression|Antibody Capture],
+
+[samples]
+sample_id,probe_barcode_ids,description
+MULTIPLEXED_SAMPLE,BC001|BC002|...,DESCRIPTION
+"""
+        out_file = os.path.join(self.wd,"10x_multi_config.csv")
+        make_multi_config_template(out_file,
+                                   reference="/data/mm10_transcriptome",
+                                   probe_set="/data/mm10_probe_set.csv",
+                                   fastq_dir="/runs/novaseq_50/fastqs",
+                                   samples=("PJB_Flex",),
+                                   no_bam=True,
+                                   library_type="Flex",
+                                   cellranger_version="9.0.0")
+        self.assertTrue(os.path.exists(out_file))
+        with open(out_file,'rt') as fp:
+            actual_content = '\n'.join([line for line in fp.read().split('\n')
+                                        if not line.startswith('##')])
+        self.assertEqual(expected_content,actual_content)
+
     def test_make_multi_config_template_immune_profiling_710(self):
         """
         make_multi_config_template: check Single Cell Immune Profiling template (7.0.0)
@@ -931,6 +1003,40 @@ def test_make_multi_config_template_immune_profiling_800(self):
                                         if not line.startswith('##')])
         self.assertEqual(expected_content,actual_content)
 
+    def test_make_multi_config_template_immune_profiling_900(self):
+        """
+        make_multi_config_template: check Single Cell Immune Profiling template (9.0.0)
+        """
+        expected_content = """[gene-expression]
+reference,/data/mm10_transcriptome
+#force-cells,n
+create-bam,true
+#cmo-set,/path/to/custom/cmo/reference
+
+#[feature]
+#reference,/path/to/feature/reference
+
+#[vdj]
+#reference,/path/to/vdj/reference
+
+[libraries]
+fastq_id,fastqs,lanes,physical_library_id,feature_types,subsample_rate
+PJB_CML,/runs/novaseq_50/fastqs,any,PJB_CML,[Gene Expression|Antibody Capture|VDJ-B|VDJ-T],
+PJB_GEX,/runs/novaseq_50/fastqs,any,PJB_GEX,[Gene Expression|Antibody Capture|VDJ-B|VDJ-T],
+"""
+        out_file = os.path.join(self.wd,"10x_multi_config.csv")
+        make_multi_config_template(out_file,
+                                   reference="/data/mm10_transcriptome",
+                                   fastq_dir="/runs/novaseq_50/fastqs",
+                                   samples=("PJB_CML","PJB_GEX"),
+                                   library_type="Single Cell Immune Profiling",
+                                   cellranger_version="9.0.0")
+        self.assertTrue(os.path.exists(out_file))
+        with open(out_file,'rt') as fp:
+            actual_content = '\n'.join([line for line in fp.read().split('\n')
+                                        if not line.startswith('##')])
+        self.assertEqual(expected_content,actual_content)
+
     def test_make_multi_config_template_unsupported_library(self):
         """
         make_multi_config_template: exception for unsupported library type