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souporcell_pipeline.py: ensure that logs subdirectory exists #278

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souporcell_pipeline.py: ensure that logs subdirectory exists #278

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6 changes: 3 additions & 3 deletions souporcell_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -611,10 +611,10 @@ def resolve_pyscript(name):
)

#### MAIN RUN SCRIPT
if os.path.isdir(args.out_dir):
if os.path.isdir(os.path.join(args.out_dir, "logs")):
print("restarting pipeline in existing directory " + args.out_dir)
else:
subprocess.check_call(["mkdir", "-p", args.out_dir + "/logs"])
os.makedirs(os.path.join(args.out_dir, "logs"), exist_ok=True)
if not args.skip_remap:
if not os.path.exists(args.out_dir + "/fastqs.done"):
(region_fastqs, all_fastqs) = make_fastqs(args)
Expand Down Expand Up @@ -657,4 +657,4 @@ def resolve_pyscript(name):
if not(os.path.exists(args.out_dir + "/consensus.done")):
consensus(args, ref_mtx, alt_mtx, doublet_file, final_vcf)
print("done")
#### END MAIN RUN SCRIPT
#### END MAIN RUN SCRIPT