Merge pull request #1225 from ComparativeGenomicsToolkit/docker-fixes

fix gfaffix dont_collapse regex

src/cactus/refmap/cactus_graphmap_join.py

@@ -552,7 +552,7 @@ def clip_vg(job, options, config, vg_path, vg_id, phase):
         cactus_call(parameters=['vg', 'convert', '-W', '-f', vg_path], outfile=gfa_in_path, job_memory=job.memory)
         fix_cmd = ['gfaffix', gfa_in_path, '--output_refined', gfa_out_path, '--check_transformation']
         if options.reference:
-            fix_cmd += ['--dont_collapse', options.reference[0] + '*']
+            fix_cmd += ['--dont_collapse', options.reference[0] + '#[.]*']
         cactus_call(parameters=fix_cmd, job_memory=job.memory)
         # GFAffix strips the header, until this is fixed we need to add it back (for the RS tag)
         gfa_header = cactus_call(parameters=['head', '-1', gfa_in_path], check_output=True).strip()