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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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R functionality in cgat #120

Closed jscaber closed 4 years ago

jscaber commented 4 years ago

This is not really a pull request but a discussion stub, disguised as a PR to enable discussion of this code.

I have tried to merge the experiment.R functionality with the existing cgatflow pipeline. I realised this may be better placed elsewhere, but as this is the most experimental repository that fewest people use, I thought placing the functionality here would be best.

cgatflow.py main now looks for the arguments "cgatflow R" and if these are present does argument parsing which ultimately leads to command line tools in a new "Rtools" subdirectory.

This would allow calling "cgatflow R tool" from the pipeline itself.

Realise this might be a little hacky so open to other suggestions.

jscaber commented 4 years ago

Specifically, question relates to commit 9c7f06a