AttributeError: 'str' object has no attribute 'resolve'.

[yangchuhua]

Hi Shujia,

Thanks for your effort in this project.

I got the following error when I wanted to generate the bash scripts for VQSR part.

$ilus VQSR     -n DZHK_WGS     -C ilus_sys.yaml     -L vcf.list     -O genotype     --as_pipe_shell_order

Traceback (most recent call last):
  File "../miniconda3/bin/ilus", line 8, in <module>
    sys.exit(main())
  File "../miniconda3/lib/python3.8/site-packages/ilus/main.py", line 183, in main
    run_command(args)
  File "../miniconda3/lib/python3.8/site-packages/ilus/main.py", line 174, in run_command
    runner[args.command](args, aione)
  File "../miniconda3/lib/python3.8/site-packages/ilus/pipeline/_wgs.py", line 250, in variantrecalibrator
    _f(kwargs, aione, shell_fname, shell_log_folder, gatk_variantrecalibrator)
  File "../miniconda3/lib/python3.8/site-packages/ilus/pipeline/_wgs.py", line 157, in _f
    kwargs.outdir = safe_makedir(kwargs.outdir.resolve())  # return abspath
AttributeError: 'str' object has no attribute 'resolve'

I have tried to replace 157 row in ../ilus/pipeline/_wgs.py :kwargs.outdir = safe_makedir(kwargs.outdir.resolve()) by kwargs.outdir = safe_makedir(Path(kwargs.outdir).resolve()) , but it didn't work.

Do you have any suggestion?

Best,
Chuhua