fix custombdr config

Snakefile

@@ -274,13 +274,13 @@ else:
     dfpmr['fasta'] = dfpmr['marker'].map(config["assign_taxon"]["fasta"])
 
 ## also perform taxonomic assignment with custom reference database
-if config['custom_bdr']['status']:
+if config['custom_baseref']:
     print("also perform taxonomic assignment with custom reference database")
-    for crmarker in config['custom_bdr']['bdr'].keys():
+    for crmarker in config['assign_customtax']['bdr'].keys():
         print(crmarker)
         df_crmarker = dfpmr[(dfpmr.marker == crmarker)].copy()
-        df_crmarker['bdr'] = config['custom_bdr']['bdr'][crmarker]
-        df_crmarker['fasta'] = config['custom_bdr']['fasta'][crmarker]
+        df_crmarker['bdr'] = config['assign_customtax']['bdr'][crmarker]
+        df_crmarker['fasta'] = config['assign_customtax']['fasta'][crmarker]
         df_crmarker['projmarkrun'] = df_crmarker['projmarkrun'].astype(str) + '_custom'
         dfpmr = pandas.concat([dfpmr, df_crmarker], ignore_index=True)    
     customprojmarkrun = dfpmr[dfpmr['projmarkrun'].str.contains('_custom')]['projmarkrun']
@@ -371,7 +371,7 @@ rule flag_filtering_done:
         touch('results/00_flags/filtering.flag')
 
 
-if config['custom_bdr']['status']:
+if config['custom_baseref']:
     rule custom_bdr_cat_samples_into_runs:
         input:
             'results/00_flags/filtering.flag'
@@ -396,7 +396,7 @@ else:
             '''
 
 include: "rules/dereplicate_runs.smk"
-if config['custom_bdr']['status']:
+if config['custom_baseref']:
     include: "rules/custom_taxonomic_assignment.smk"
 else:
     include: "rules/taxonomic_assignment.smk"
@@ -418,7 +418,10 @@ rule flag_table_assigned_sequences:
             thisMarker = pmr.split('/')[1]
             thisRun = pmr.split('/')[2]
             tableNameFile = "results/18_table_assigned_sequences/"+pmr+".csv"
-            newTableNameFile = "results/"+thisProjet+"_"+thisMarker+"_"+thisRun+"_ecotag_ncbi.csv"
+            if "custom" in thisRun:
+                newTableNameFile = "results/"+thisProjet+"_"+thisMarker+"_"+thisRun+"_ecotag.csv"
+            else:
+                newTableNameFile = "results/"+thisProjet+"_"+thisMarker+"_"+thisRun+"_ncbi_ecotag.csv"
             print(thisProjet+"_"+thisMarker+"_"+thisRun+", ", end='')
             os.system("cp {0} {1}".format(tableNameFile, newTableNameFile))
         print("done")