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biocore / mg-scripts

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal
BSD 3-Clause "New" or "Revised" License
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Confirm Qiita Study sample-templates do not already contain well_id_384 and other reserved columns. #150

Closed charles-cowart closed 1 month ago

charles-cowart commented 2 months ago

Retrieve the qiita study id from the provided sample-sheet at the start of an SPP job and use it to retrieve the list of columns existing in the study's sample-template. If columns are found with names identical to those found in prep-info files, raise an Error message to the user letting them know the offending column(s) and abort early.

This is a sanity check to prevent a job running 3/4s of the way to completion only to fail when SPP is attempting to load preps into Qiita.

Additional column names can be added to the confirmation code as needed.

This issue supersedes https://github.com/qiita-spots/qiita/issues/3429

charles-cowart commented 1 month ago

The solution is broken up into two parts - an additional function to the SPP plugin that performs much of the work and a helper function in mg-scripts that generates the list of reserved words.

The PR for the SPP plugin is here: https://github.com/qiita-spots/qp-knight-lab-processing/pull/91

antgonza commented 1 month ago

Could you link this issue with the PR using the Development tab on the right?

charles-cowart commented 1 month ago

A PR for mg-scripts was also issued: https://github.com/biocore/mg-scripts/pull/151