Adjust import workflow configuration to support S3 #357
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input_path
, for the import workflow, to be an S3 URI.The result is that the Nextflow procedure to import a curated dataset into the database pretty much works as-is when the source files come from a folder in an S3 bucket, rather than from a local directory.
Note that Nextflow does support S3 "out of the box", but a subtlety is that it does not support the session-specific tokens that we have been using in the shell environment. Instead, in the session-specific case one must use the credentials from a user profile, and one must not allow Nextflow to try guessing credentials environment variables, because it will fail with a misleading error.