Add manual detection of endness if not stored

workflow/rna-seq.nf

@@ -116,6 +116,7 @@ process parseMetadata {
 
   output:
     val ends
+    val endsManual
     val stranded
     val spike
     val specie
@@ -133,6 +134,15 @@ process parseMetadata {
     ends=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p ends)
     echo "LOG: endedness metadata parsed: \${ends}" >>${repRID}.parseMetadata.err
     
+    # Manually get endness
+    endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${fileMeta}" -p endsManual)
+    echo "LOG: endedness manually detected: \${ends}" >>${repRID}.parseMetadata.err
+    if [ \${ends} == "uk" ]
+    then
+      ends=\${endsManual}
+      echo "LOG: endness metadata overwitten my manually detected" >>${repRID}.parseMetadata.err
+    fi
+
     # Get strandedness metadata
     stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettingsMeta}" -p stranded)
     echo "LOG: strandedness metadata parsed: \${stranded}" >>${repRID}.parseMetadata.err

workflow/scripts/parseMeta.py

@@ -33,10 +33,18 @@ def main():
             ends = "se"
         elif (metaFile.Paired_End.unique() == "Paired End"):
             ends = "pe"
+        elif (metaFile.Paired_End.unique() == ""):
+            ends = "uk"
         else:
             print("Ends metadata not match expected options: " + metaFile.Paired_End.unique())
             exit(1)
         print(ends)
+    if (args.parameter == "endsManual"):
+        if (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 1):
+            endsManual = "se"
+        elif (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 2):
+            endsManual = "pe"
+        print(endsManual)
     if (args.parameter == "stranded"):
         if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
             stranded = "stranded"