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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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Include rules for intermediate steps? (Closed: everything rule only) #21

Closed charlesreid1 closed 6 years ago

charlesreid1 commented 6 years ago

Relates to #17 ghost make all rules, and deciding how and when to make these rules.

Do we provide the user with a ghost "make all" rule for each intermediate step? Or just provide one ghost "make all" rule for the very last step of the workflow?

(Note that using this ghost rule approach, we define the endpoint and let Snakemake determine the starting point, based on what files are present.)

Do we want users to be able to run

snakemake step1
snakemake step2
snakemake step3
...

or just run

snakemake everything

?

charlesreid1 commented 6 years ago

Stick with snakemake everything for now.