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microbiomedata / mg_annotation

Metagenome Annotation Workflow
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copy output files #6

Closed mflynn-lanl closed 1 year ago

mflynn-lanl commented 3 years ago

The edge-nmdc website needs to display the output files for the annotation workflow. Currently, the output files for the mg-annotation workflow remain within the cromwell-execution directory after each task is completed. A task is needed to copy files from the cromwell-execution directory to a directory in edge_app/nmdc-edge/projects. This includes adding outdir as an optional input to the wdl and inputs.json files

mflynn-lanl commented 3 years ago

I will add a boolean copy_outputs that defaults to false so existing deployments of the workflow won't break.

aclum commented 1 year ago

@mflynn-lanl can this issue be deprecated in favor of plans to use the jaws API to fetch the data? Being able to have the WDLs run across computing sites is in conflict with specifying an final output directory within the workflow since where the compute is done and where edge needs the files to display them may be different.

mflynn-lanl commented 1 year ago

Yes, that’s fine

From: aclum @.> Reply-To: microbiomedata/mg_annotation @.> Date: Monday, January 23, 2023 at 12:08 PM To: microbiomedata/mg_annotation @.> Cc: "Flynn, Mark C" @.>, Mention @.***> Subject: [EXTERNAL] Re: [microbiomedata/mg_annotation] copy output files (#6)

@mflynn-lanlhttps://urldefense.com/v3/__https:/github.com/mflynn-lanl__;!!Bt8fGhp8LhKGRg!Dtwd9RqeL2nQqaS-PQh2uyaqDw9FiXLZI47KzFRlVKjRnYMMtrczygsYyWRb7SQ673C3Bc5E0u42OMkyJK824P9R$ can this issue be deprecated in favor of plans to use the jaws API to fetch the data? Being able to have the WDLs run across computing sites is in conflict with specifying an final output directory within the workflow since where the compute is done and where edge needs the files to display them may be different.

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