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microbiomedata / metaT

Metatranscriptomics workflow
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copy output.json file from cromwell-executions to an output directory #11

Closed mflynn-lanl closed 3 years ago

mflynn-lanl commented 3 years ago

We need to add to the wdl file is some way of copying the output.json file out of cromwell-executions. In the README, it has instructions for executing the workflow in run mode. While this is fine for testing, it doesn’t work in production. We will be using server mode for running metaT for NMDC EDGE as well as for other deployments. Executing the workflow in run mode has the -m option for specifying an output file, which is not available in server mode. Just like for ReadbasedAnalysis, we will need to copy the output.json file to some output directory.

mflynn-lanl commented 3 years ago

We will need add an output directory to the input.json file as well

mshakya commented 3 years ago

Thanks @mflynn-lanl, I added this feature to the latest full version. I tested and it worked. I am closing the issue, but can reopen later if need be.