Commit ea23018f authored by aknecht2's avatar aknecht2
Browse files

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

parent 8f82cd13
......@@ -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"]
}
......
......@@ -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:
......
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