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farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
https://gentb.hms.harvard.edu
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Implement user feedback of error and quality for other pipelines e.g. single ended pipeline, VCF pipeline #233

Closed mahafarhat closed 3 years ago

mahafarhat commented 3 years ago

At the moment when single-ended, or VCF file jobs fail little to no user feedback of error is given to the user. We need to implement the same changes we did for paired end pipelines

doctormo commented 3 years ago

Do you mean add the quality control flag to the single end and vcf pipeline jobs? This checkbox but for some of those pipeline jobs?

Screenshot from 2021-04-15 13-35-32

Otherwise, I'm not sure. There's nothing in the code that's special to pair-ended jobs at the moment.

mahafarhat commented 3 years ago

I'm referring to the fact that the program error message is not displayed to the user when a program step fails. e.g. if a job fails quality control they just get a generic job failed for these two pipelines.

doctormo commented 3 years ago

I don't understand Maha. Sorry. I've checked the quality control information and it seems to all be correct.

Can you explain with the screenshot?