Updated bwa additional files. Adjusted file naming in genome checking.

chipathlon/conf.py

@@ -17,7 +17,7 @@ file_extensions = {
     "sam": ["sam"],
     "bam": ["bam"],
     "bed": ["bed", "narrowPeak", "broadPeak"],
-    "bwa_genome": ["amb", "ann", "bwt", "pac", "sac"],
+    "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
     "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"]
 }
 

chipathlon/workflow.py

@@ -172,13 +172,13 @@ class Workflow(object):
                             if not os.path.isfile(prefix + "." + ext) and not os.path.isfile(base_file + "." + ext):
                                 missing.append(ext)
                             else:
-                                f = File(gen_prefix + "." + ext)
+                                fnew = File(gen_prefix + "." + ext)
                                 if os.path.isfile(prefix + "." + ext):
-                                    f.addPFN(prefix + "." + ext)
+                                    fnew.addPFN(prefix + "." + ext)
                                 else:
-                                    f.addPFN(base_file + "." + ext)
-                                self.files[gen_prefix + "." + ext] = f
-                                self.dax.addFile(f)
+                                    fnew.addPFN(base_file + "." + ext)
+                                self.files[gen_prefix + "." + ext] = fnew
+                                self.dax.addFile(fnew)
                         if len(missing) > 0:
                             self.err += "Genome defined with tool '%s' and assembly '%s' is missing additional_files with extensions %s.\n" % (run["align"], assembly, missing)
                     else: