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biocore / oecophylla

shotgun pipeline
MIT License
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WIP: launch script skeleton #67

Closed tkosciol closed 7 years ago

tkosciol commented 7 years ago

Skeleton of the launch script. Once ready, we want to be able to run an entire pipeline and specify parameters from 1 script. Example usage:

Installation:

oecophylla install

Execute Workflow:

oecophylla workflow --input-dir ./inputs --sample-sheet sample.txt --params params.yaml --output-dir ./outputs

tkosciol commented 7 years ago

@jwdebelius check out what we're looking for as install functionality. On top of oecophylla install we want to be able to specify --config-file which would explicitly define conda modules and/or local modules

tkosciol commented 7 years ago

@mortonjt I think you can close this PR, as all of the code and comments are addressed by your PR #77 , right?