Documentation and config errors

[stasys-hub]

Hello, thank you very much for this pipeline!

Albeit beeing awesome to have something like this, I would really appreciate some more documentation. Especially on configuring and running the pipeline. I have immense problems to getting this running with our benchmark data, because i am getting cryptic snakemake errors which are hard to decipher.

For example I just adapted the config files and I have no clue what this should tell me:

snakemake --use-conda -n
AttributeError in line 27 of /home/stasys/Projects/Pore-C-Snakemake/rules/common.smk:
Can only use .str accessor with string values!
  File "/home/stasys/Projects/Pore-C-Snakemake/Snakefile", line 28, in <module>
  File "/home/stasys/Projects/Pore-C-Snakemake/rules/common.smk", line 27, in create_config_dataframes
  File "/home/stasys/miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/pandas/core/generic.py", line 5270, in __getattr__
  File "/home/stasys/miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/pandas/core/accessor.py", line 187, in __get__
  File "/home/stasys/miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/pandas/core/strings.py", line 2041, in __init__
  File "/home/stasys/miniconda3/envs/pore-c-snakemake/lib/python3.8/site-packages/pandas/core/strings.py", line 2098, in _validate

This error just tells me that somehow pandas tries to replace something in a non-string column with a string.

Also I am not really convinced by the design choice of using TSVs as a config file, which leads to horrific formation which made me a lot of problems. Especially if someone has an IDE config which replaces tabs with spaces. This seems to be quite error prone. Why not use a toml or yaml file? Command line arguments would also be fine. Then one just saves his variables in a bash script.