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AlexsLemonade / OpenScPCA-nf

A workflow for running OpenScPCA analysis modules
BSD 3-Clause "New" or "Revised" License
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Add data release as workflow dispatch option #61

Closed jashapiro closed 4 months ago

jashapiro commented 4 months ago

Closes #60

Since the primary method of running the openscpca-nf workflow will be via workflow dispatch, I wanted to add the ability to specify a data release to the options there, so this PR does that. In particular, we may want to run on "future" releases during the process of preparing a new data release.

As with other arguments, the value is passed along via setting an environment variable in the tmux launch script before sending it to AWS.

The release is only used for the simulate entrypoint or when running the rest of the workflow with real data, to prevent overwriting the prefix for test data.

I also added a check that the release prefix is valid, so we don't waste time trying to launch a workflow when the input directory doesn't exist. If that and/or the nextflow pull fails, we report the error and exit.

jashapiro commented 4 months ago

I'm not sure if that's true, but I suppose we will find out.

See my other PR... I'm not sure either!