Corrected tests after adding more details in qcData sequencing_metrics

Author: nkongenelly

checkQC/parsers/illumina.py

@@ -36,7 +36,6 @@ def from_bclconvert(cls, runfolder_path, parser_config):
     sequencing_metrics = {
         lane + 1: {
             "total_cluster_pf": summary.at(0).at(lane).reads_pf(),
-            "total_cluster": summary.at(0).at(lane).reads(),
             "pf_clusters": summary.at(0).at(lane).cluster_count_pf().mean(),
             "raw_clusters": summary.at(0).at(lane).cluster_count().mean(),
             "raw_density":summary.at(0).at(lane).density().mean(),

requirements/prod

@@ -1,10 +1,10 @@
 click~=8.1.1
 PyYAML~=6.0
-interop~=1.3.2
+interop~=1.4.0
 xmltodict~=0.13.0
 tornado~=6.3.2
 sample_sheet~=0.13.0
 pandas~=2.2.2
-numpy~=1.26.4
+numpy~=2.2.4
 samshee~=0.2.3
 jsonschema~=4.23.0

setup.py

@@ -11,14 +11,19 @@
     author_email='[email protected]',
     url="https://www.github.com/Molmed/checkQC",
     download_url='https://github.com/Molmed/checkQC/archive/{}.tar.gz'.format(__version__),
-    python_requires='>3.10, <3.11',
+    python_requires='>3.10',
     install_requires=[
-        "click",
-        "PyYAML>=6.0",
-        "interop>=1.2.4",
-        "xmltodict",
-        "tornado",
-        "sample_sheet"],
+        "click~=8.1.1",
+        "PyYAML~=6.0",
+        "interop~=1.4.0",
+       " xmltodict~=0.13.0",
+        "tornado~=6.3.2",
+       " sample_sheet~=0.13.0",
+       " pandas~=2.2.2",
+        "numpy~=2.2.4",
+        "samshee~=0.2.3",
+        "jsonschema~=4.23.0",
+    ],
     packages=find_packages(exclude=["tests*"]),
     test_suite="tests",
     package_data={

tests/parsers/test_illumina_parser.py

@@ -107,4 +107,5 @@ def test_read_samplesheet(runfolder_path):
         'lane': 1,
         'sample_id': 'Sample_14574-Qiagen-IndexSet1-SP-Lane1',
         'sample_project': 'AB-1234',
+        'description': 'LIBRARY_NAME:test',
     }

tests/resources/bclconvert/200624_A00834_0183_BHMTFYTINY/SampleSheet.csv

@@ -18,7 +18,7 @@ FastqCompressionFormat,gzip,,
 SoftwareVersion,4.1.5,,
 ,,,
 [BCLConvert_Data],,,
-Lane,Sample_ID,Index,Index2,Sample_Project, Description
+Lane,Sample_ID,Index,Index2,Sample_Project,Description
 1,Sample_14574-Qiagen-IndexSet1-SP-Lane1,GAACTGAGCG,TCGTGGAGCG,AB-1234,LIBRARY_NAME:test
 1,Sample_14575-Qiagen-IndexSet1-SP-Lane1,AGGTCAGATA,CTACAAGATA,CD-5678,LIBRARY_NAME:test
 2,Sample_14574-Qiagen-IndexSet1-SP-Lane2,GAACTGAGCG,TCGTGGAGCG,AB-1234,LIBRARY_NAME:test

tests/test_qc_data.py

@@ -35,33 +35,41 @@ def bclconvert_runfolder():
                     "index": "GAACTGAGCG",
                     "index2": "TCGTGGAGCG",
                     "sample_project": "AB-1234",
+                    "description": "LIBRARY_NAME:test",
                 },
                 {
                     "lane": 1,
                     "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane1",
                     "index": "AGGTCAGATA",
                     "index2": "CTACAAGATA",
                     "sample_project": "CD-5678",
+                    "description": "LIBRARY_NAME:test",
                 },
                 {
                     "lane": 2,
                     "sample_id": "Sample_14574-Qiagen-IndexSet1-SP-Lane2",
                     "index": "GAACTGAGCG",
                     "index2": "TCGTGGAGCG",
                     "sample_project": "AB-1234",
+                    "description": "LIBRARY_NAME:test",
                 },
                 {
                     "lane": 2,
                     "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane2",
                     "index": "AGGTCAGATA",
                     "index2": "CTACAAGATA",
                     "sample_project": "CD-5678",
+                    "description": "LIBRARY_NAME:test",
                 },
             ],
         },
         "expected_sequencing_metrics": {
             1: {
                 "total_cluster_pf": 532_464_327,
+                "pf_clusters": 3_413_232.5,
+                "raw_clusters": 4_091_904.0,
+                "raw_density": 2_961_270.5,
+                "pf_density": 2_470_118.25,
                 "yield": 122_605_416,
                 "yield_undetermined": 121_940_136,
                 "top_unknown_barcodes": {
@@ -113,15 +121,27 @@ def bclconvert_runfolder():
                     {
                         "sample_id": "Sample_14574-Qiagen-IndexSet1-SP-Lane1",
                         "cluster_count": 9920,
+                        "percent_of_lane": 0.29,
+                        "percent_perfect_index_reads": 97.96,
+                        "mean_q30": 36.37,
+                        "percent_q30": 0.96,
                     },
                     {
                         "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane1",
                         "cluster_count": 8560,
+                        "percent_of_lane": 0.25,
+                        "percent_perfect_index_reads": 98.15,
+                        "mean_q30": 36.43,
+                        "percent_q30": 0.96,
                     },
                 ],
             },
             2: {
                 "total_cluster_pf": 530_917_565,
+                "pf_clusters": 3_403_318.25,
+                "raw_clusters": 4_091_904.0,
+                "raw_density": 2_961_270.5,
+                "pf_density": 2_462_942.5,
                 "yield": 124_497_108,
                 "yield_undetermined": 123_817_428,
                 "top_unknown_barcodes": {
@@ -173,10 +193,18 @@ def bclconvert_runfolder():
                     {
                         "sample_id": "Sample_14574-Qiagen-IndexSet1-SP-Lane2",
                         "cluster_count": 10208,
+                        "percent_of_lane": 0.3,
+                        "percent_perfect_index_reads": 98.2,
+                        "mean_q30": 36.4,
+                        "percent_q30": 0.96,
                     },
                     {
                         "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane2",
                         "cluster_count": 8672,
+                        "percent_of_lane": 0.25,
+                        "percent_perfect_index_reads": 98.29,
+                        "mean_q30": 36.48,
+                        "percent_q30": 0.97,
                     },
                 ],
             },