Can't run pipeline. Problem recognizing fastq?

[fbleao]

Hi,
I installed the latest version of capcruncher as suggested and I'm currently trying to run it. I'm getting the following error:

TypeError in file /home/linux/miniforge3/lib/python3.10/site-packages/capcruncher/pipeline/workflow/Snakefile, line 32:
expected str, bytes or os.PathLike object, not float
File "/home/linux/miniforge3/lib/python3.10/site-packages/capcruncher/pipeline/workflow/Snakefile", line 32, in
File "/home/linux/miniforge3/lib/python3.10/site-packages/capcruncher/pipeline/utils.py", line 199, in from_files
File "/home/linux/miniforge3/lib/python3.10/site-packages/pandas/core/series.py", line 4626, in apply
File "/home/linux/miniforge3/lib/python3.10/site-packages/pandas/core/apply.py", line 1025, in apply
File "/home/linux/miniforge3/lib/python3.10/site-packages/pandas/core/apply.py", line 1076, in apply_standard
File "pandas/_libs/lib.pyx", line 2834, in pandas._libs.lib.map_infer
File "/home/linux/miniforge3/lib/python3.10/site-packages/capcruncher/pipeline/utils.py", line 202, in
File "/home/linux/miniforge3/lib/python3.10/posixpath.py", line 142, in basename

My fastq and config files are in the same working directory. Any ideas what the issue might be?

Thank you!

[Mingwan2002]

Hi fbleao!

I faced the exact same issue!

I tried placing the config.yml file both with the compressed and catenated data, and in another folder, but both did not work.

I've put my error beside yours (on NotePad), most lines are similar!

Hopefully, it can be resolved soon

[MaxMLang]

I'm also getting the same error however I got it to work past that point (although not completely) by automatically recognising the files by naming them as suggested in the Docs and placing the config.yml in the same directory.