Sample-sheet assay-type will now be verified.

charles-cowart commented 1 year ago

Legal values are currently ('TruSeq HT', 'Metagenomic'). Popular alternative 'Metagenomics' will now return an error to the user.

charles-cowart commented 1 year ago

Hi @wasade! Since @antgonza is away, would you mind reviewing this pull-request please? If and when it's approved I will test it on qiita-rc and then introduce it to production as a hot-fix. We are getting a number of sample-sheet submissions with a value that is no longer valid and causes a cryptic error message to be returned. Thanks!

coveralls commented 1 year ago

Pull Request Test Coverage Report for Build 4615367301

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

24 of 24 (100.0%) changed or added relevant lines in 4 files are covered.
34 unchanged lines in 2 files lost coverage.
Overall coverage increased (+0.2%) to 82.707%

Files with Coverage Reduction	New Missed Lines	%
sequence_processing_pipeline/Pipeline.py	12	86.76%
sequence_processing_pipeline/QCJob.py	22	75.7%
<!--	Total:	34	-->

Totals
Change from base Build 4538408751:	0.2%
Covered Lines:	1516
Relevant Lines:	1719

💛 - Coveralls

charles-cowart commented 1 year ago

Although the sanity-check in QCJob should remain, I realized it would be better to detect and report the error when sample-sheet validation is performed.

charles-cowart commented 1 year ago

@wasade Thanks! Ready for review!

wasade commented 1 year ago

Thanks!!

biocore / mg-scripts