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Inconsistent naming of parameters in Snakefile and parameters.yaml #5

Closed katkopera closed 1 year ago

katkopera commented 1 year ago

I've noticed inconsistency in parameter naming between Snakefile and parameters.yaml

In rule filter_adapters: params: trim_exec = config['trim_exec'], trim_adapters = config['adapters'], minqual = config['minqual'],

Snakefile expects 'trimmomatic_exec' while in parameters.yaml there is 'trim_exec'. Snakefile expects 'adapters' while in parameters.yaml there is 'trim_adapters'.

This leads to KeyErrors. Please fix.

tommyfuu commented 1 year ago

hi,

Sorry about that - that was due to a previous commit not consistent with the rest of the repo.

It should now be fixed - check out config/parameters.yaml for the file. If you want an example of these file paths, check out test_data/parameters.yaml.

Let me know if you have any more questions.

lauren-mak commented 1 year ago

This has been addressed in the latest update (version 0.7.0). Please pull it, go over the README.md to make sure the module has been set up properly, and see if it works. Thanks for using the CAMP short-read QC module!