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Output Directory is Deleted #4

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DarioS opened this issue Jul 9, 2024 · 0 comments

DarioS commented Jul 9, 2024

I specified . as output directory by --output . It fails

  File "/usr/lib/python3.11/shutil.py", line 736, in rmtree
    os.rmdir(path, dir_fd=dir_fd)
OSError: [Errno 22] Invalid argument: '.'

It also deletes the contents of the directory!

$ ls
copyNs.txt  shortVs.txt
$ python rungritic_cmd.py --mutation_table shortVs.txt --copy_number_table copyNs.txt --purity 0.25 \
  --sample_id test --output . --wgd_status T
# Error here
$ ls
$

Poor user documentation and software design.

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