Make unitas work without refseq args

Author: kieranr51

hlsmallrna/__main__.py

@@ -190,8 +190,10 @@ def unitas_command(small_rna_path, species_name, ref_seqs, cds, unspliced_transc
 
     mkdir_if_not_exists(UNITAS_OUTPUT)
 
+    small_rna_list = glob.glob(os.path.join(small_rna_path, '*.fastq'))
+
     with Pool(threads, initializer=init_worker, initargs=(species_name, ref_seqs, quiet, UNITAS_OUTPUT,)) as p:
-        p.map(unitas_threads, glob.glob(os.path.join(small_rna_path, '*.fastq')))
+        p.map(unitas_threads, small_rna_list)
 
     table_path = merge_summary()
     graph_unitas_classification_type(table_path)

hlsmallrna/unitas.py

@@ -59,9 +59,10 @@ def run_unitas_annotation(small_rna, species_name, ref_files, quiet=0, unitas_ou
         '-species', species_name
     ]
 
-    for refs in ref_files:
-        unitas_command.append('-refseq')
-        unitas_command.append(os.path.join(CWD, refs))
+    if ref_files is not None:
+        for refs in ref_files:
+            unitas_command.append('-refseq')
+            unitas_command.append(os.path.join(CWD, refs))
 
     unitas_command = unitas_command + get_config_key('cli-tools', 'unitas', 'unitas_params')