dahak-metagenomics / dahak-taco

🌮 Taco is an experimental command line interface for dahak workflows. https://dahak-metagenomics.github.io/dahak-taco
BSD 3-Clause "New" or "Revised" License
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Improve command line interface #9

Open charlesreid1 opened 6 years ago

charlesreid1 commented 6 years ago

Suggestions from Titus:

Have 2 equivalent ways to run things:

A short and sweet command that infers file structure:

% taco workflow1 my-workflow-files

A longer and more explicit command:

% taco workflow1 --config-yaml=-my-workflow-files/config.yaml --params-yaml=my-workflow-files/params.yaml

A third, optimal, but more difficult way is to let the user provide a list of input files:

% taco workflow1 --input-files <list of files>
charlesreid1 commented 6 years ago

This is a broader issue than #13 (eliminate redundancy) but that's an important first step

charlesreid1 commented 6 years ago

To infer structure,

$ taco workflow1 my-workflow-files

could just glob.glob("my-workflow-files/*conf*") and glob.glob("my-workflow-files/*params*") and assert both have only 1 element.