Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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replace coverm #11

Closed beardymcjohnface closed 1 year ago

beardymcjohnface commented 1 year ago

Replaces coverm. I also added resources to the config file. Just be aware that resources in the config is multi-level and if you want to make it parseable on the command line AND mergeable with the default config you'll need to replace the config merge funcion with a recursive one. the one we use for hecatomb is:

import collections.abc
def recursive_merge_config(config, overwrite_config):
    def _update(d, u):
        for (key, value) in u.items():
            if isinstance(value, collections.abc.Mapping):
                d[key] = _update(d.get(key, {}), value)
            else:
                d[key] = value
        return d
    _update(config, overwrite_config)