star-fusion

HudsonAlpha · Dec 2, 2016 · fcdce17 · fcdce17
1 parent 1f1781f
commit fcdce17
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/lib/programs.py b/lib/programs.py
@@ -291,10 +291,9 @@ def starfusion(timestamp, path_base, folder, samples, nproc, wt, q, path_star_fu
             fn = [g + files[0].split("/")[-1] + suf, g + files[1].split("/")[-1] + suf]
         prefix = path_base + folder + "/results_star-fusion/" + sample
         call = config.path_starfusion + " --output_dir " + prefix + " --genome_lib_dir " + path_star_fusion + " --left_fq " + fn[0] + " --right_fq " + fn[1] + " --CPU " + str(nproc)
-        commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_star-fusion").replace("#SAMPLE", sample))
         if len(star_fusion_params) > 0:
             command = command + star_fusion_params
-        commands.append(command + sample_checker.replace("#FOLDER", path_base + folder + "/results_star-fusion").replace("#SAMPLE", sample))
+        commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_star-fusion").replace("#SAMPLE", sample))
     create_scripts(nchild, commands, path_base, folder, output)
     return submit_job_super("star-fusion", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)