Proposal: Rewrite SRA_RUNINFO_TO_FTP as native process#337
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bentsherman wants to merge 1 commit intodevfrom
Open
Proposal: Rewrite SRA_RUNINFO_TO_FTP as native process#337bentsherman wants to merge 1 commit intodevfrom
bentsherman wants to merge 1 commit intodevfrom
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Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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Just a POC to demonstrate how to rewrite a simple process as an
execprocess.The
SRA_RUNINFO_TO_FTPprocess just transforms a metadata file and doesn't make any network requests, so it can be written purely in Nextflow pretty easily. That way you don't have to spin up a Python job just to do some metadata wrangling.I think most people don't realize you can do this, due to the (historically) poor developer experience and lack of standard library documentation. Between the new strict syntax and upcoming standard library docs, I'm hoping people might find this approach more appealing.
A further optimization would be to not even write the samplesheet to a TSV file -- just emit the samplesheet as a list of maps.