Default 'do_' lend themselves to be bools rather than strings ?

[WardDeb]

These are set as default:

info_dict["do_basecall"] = config["default_process"]["do_basecall"]
info_dict["do_align"] = config["default_process"]["do_align"]
info_dict["do_modbed"] = config["default_process"]["do_modbed"]

and written as strings in the config, while from just glancing over the code could just be bools ?

[adRn-s]

Just for context: YAML spec had changed what's interpreted as boolean across versions. So, parsers may do different things and still be correct. Python's parser should be fine.

I actually implemented these as "YES" and "NO" strings, with a bash hattrick to convert variables to uppercase. I don't recall what the issue was, but it was working until it didn't... so, there's that. Perhaps @caballero can provide some context, as he had to revert my changes to move forward with a flowcell back then.

[caballero]

we tried using yes/no and true/false, there are incorrect interpretation at different levels in python/snakemake code, so I preferred to roll back to use a string

[WardDeb]

I'm not sure I follow, bools from yaml seem to work, as this is how verbosity is set. This could get awkward if the conditionals are used within shell, but imo that should be avoided cfr. #192