Refactored code

Author: nkongenelly

bin/get_metadata.py

@@ -14,7 +14,7 @@
 
 
 class RunfolderInfo:
-    def __init__(self, runfolder, demultiplexer_outdir):
+    def __init__(self, runfolder):
         self.runfolder = runfolder
         self.run_info = self.read_run_info()
         self.run_parameters = self.read_run_parameters()
@@ -158,9 +158,8 @@ def get_demultiplexing_info(self):
 
     args = parser.parse_args()
     runfolder = args.runfolder
-    demultiplexer_outdir = args.demultiplexer_outdir
 
-    runfolder_info = RunfolderInfo(runfolder, demultiplexer_outdir)
+    runfolder_info = RunfolderInfo(runfolder)
     info = runfolder_info.get_info()
 
     print(

main.nf

@@ -257,14 +257,9 @@ process GET_METADATA {
     path 'sequencing_metadata_mqc.yaml'
 
     script:
-    if ( params.demultiplexer_outdir ){
-        demultiplexer_outdir_section = "--demultiplexer-outdir ${params.demultiplexer_outdir}"
-    } else {
-        demultiplexer_outdir_section = ""
-    }
     """
     python ${params.script_dir}/get_metadata.py --runfolder $runfolder \\
-        $demultiplexer_outdir_section &> sequencing_metadata_mqc.yaml
+        &> sequencing_metadata_mqc.yaml
     """
 }
 

tests/unit_tests/test_get_metadata.py

@@ -13,7 +13,7 @@
 
 @pytest.fixture
 def runfolder_info():
-    return RunfolderInfo("test_data/210510_M03910_0104_000000000-JHGJL", "Unaligned")
+    return RunfolderInfo("test_data/210510_M03910_0104_000000000-JHGJL")
 
 
 @pytest.fixture
@@ -64,24 +64,18 @@ def test_get_run_parameters(runfolder_info):
 
 
 def test_run_parameters_novaseq_x():
-    runfolder_info = RunfolderInfo(
-        "test_data/20230125_lh00103_0036_A222VGWLT3", "Unaligned"
-    )
+    runfolder_info = RunfolderInfo("test_data/20230125_lh00103_0036_A222VGWLT3")
     filtered_run_parameters = runfolder_info.get_run_parameters()
     assert filtered_run_parameters["Instrument type"] == "NovaSeqXPlus"
     assert filtered_run_parameters["Control software"] == "control-software"
     assert filtered_run_parameters["Control software version"] == "1.0.0.4155"
 
 
 def test_find_flowcell_type_novaseqx():
-    runfolder_info = RunfolderInfo(
-        "test_data/20230125_lh00103_0036_A222VGWLT3", "Unaligned"
-    )
+    runfolder_info = RunfolderInfo("test_data/20230125_lh00103_0036_A222VGWLT3")
     flowcell_type = runfolder_info.find_flowcell_type_novaseqx()
     assert flowcell_type["Flowcell type"] == "10B"
-    runfolder_info = RunfolderInfo(
-        "test_data/210510_M03910_0104_000000000-JHGJL", "Unaligned"
-    )
+    runfolder_info = RunfolderInfo("test_data/210510_M03910_0104_000000000-JHGJL")
     flowcell_type = runfolder_info.find_flowcell_type_novaseqx()
     assert flowcell_type is None