Parkourtest (#208)

README.md

@@ -12,7 +12,7 @@ Clone this repository, create the environment and pip install
 
  > git clone git@github.com:maxplanck-ie/dissectBCL.git  
  > cd dissectBCL  
- > conda create -f env.yml --name dissectBCL  
+ > conda env create -f env.yml --name dissectBCL  
  > conda activate dissectBCL  
  > pip install ./  
 

src/dissectBCL/fakeNews.py

@@ -443,7 +443,7 @@ def gatherFinalMetrics(outLane, flowcell):
         # hence the try / except.
         # 'mouse (GRCm39)' -> 'mouse'
         parkourOrg = str(  # To string since NA is a float
-                ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0]
+                ssdf[ssdf["Sample_ID"] == sampleID]['Organism'].values[0][0]
             ).split(' ')[0]
         try:
             screenDF = pd.read_csv(
@@ -478,4 +478,4 @@ def gatherFinalMetrics(outLane, flowcell):
         'transferTime': flowcell.transferTime,
         'exitStats': flowcell.exitStats,
         'P5RC':ssDic['P5RC']
-    }
+    }

src/dissectBCL/misc.py

@@ -510,7 +510,7 @@ def multiQC_yaml(flowcell, project, laneFolder):
     ))
     # Organisms
     orgs = ', '.join(list(
-        ssdf["Organism"].fillna('None').unique()
+        ssdf["Organism"].str[0].fillna('None').unique()
     ))
     # Resequencing runs are screwed up (e.g. don't contain the samples)
     # switch total requested to NA
@@ -663,4 +663,4 @@ def matchOptdupsReqs(optDups, ssdf):
                     int(got)
                 ]
             )
-    return (sorted(_optDups, key=lambda x: x[1]))
+    return (sorted(_optDups, key=lambda x: x[1]))