Simplify input datasets in CLI

tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

https://nanocompore.rna.rocks

GNU General Public License v3.0

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Simplify input datasets in CLI #57

Closed a-slide closed 5 years ago

a-slide commented 5 years ago

What do you think of having an imput YAML file instead of the 4 options required at the moment ?

sample1:
    rep1:   path/to/sample1/rep1/data
    rep2:   path/to/sample1/rep2/data
sample2:
    rep1:   path/to/sample2/rep1/data
    rep2:   path/to/sample2/rep2/data

It would be parsed directly as required by nanocompore

a-slide commented 5 years ago

Implemented by https://github.com/tleonardi/nanocompore/commit/33d4bf5ba9541f3963f7afd04a889e072177b66e for both API and CLI in doc branch. Tested with sample YAML file (in docs/demo/)