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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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ghost Snakemake all rules #17

Closed charlesreid1 closed 6 years ago

charlesreid1 commented 6 years ago

a la spacegraphcats (link?):

add a rule that takes what the user wants to provide (input files) and maps to what snakemake wants the user to provide (output files).

this keeps everyone happy: the user provides input files like a normal sane human being, and snakemake gets output files, which it can use to build the task graph.

ctb commented 6 years ago

On Fri, May 11, 2018 at 04:25:17AM -0700, Chaz Reid wrote:

a la spacegraphcats (link?):

https://github.com/spacegraphcats/spacegraphcats/blob/master/conf/Snakefile#L59

charlesreid1 commented 6 years ago

This is a nice interface to provide: various named Snakemake targets.

User can specify a named target in their workflow config file. Their list of input files is moved to the parameters, and the user is no longer specifying filenames for targets.

The ghost target rule would take an input file pattern or a list of input files from the parameters file, and assemble that into file names that it specifies as inputs to the rule (no outputs).