Tapestry

I would still like to put these repositories in a GitHub repo to use them instead of using the Arvados Git repo but a test run using the Arvados repos works. The results of running the 'abe.vcf' input file can be seen at:

https://workbench.su92l.arvadosapi.com/collections/4ff0aefdcd5c9d187fd27b57f78c3a2f+1742/clinvar-report.html?disposition=inline&size=1895

Original pipeline template:

https://workbench.su92l.arvadosapi.com/pipeline_templates/su92l-p5p6p-oopbp7ikcycckcw

The Bootstrap Table (MIT/expat license?) was used to generate the table, have filtered and sortable columns. It's 'bare bones' but should be rich enough to get useful feedback on.

I've tested the other test VCF and had it run with success.

This pipeline along with it's corresponding code has been created and can be reviewed.

Two GitHub repositories have been created:

• https://github.com/abeconnelly/ClinVarReport
• https://github.com/abeconnelly/ClinVarReportHTML

Where the first generates the JSON report and the second creates the HTML for display. Thought ClinVarReportHTML doesn't do anything other than copy the relevant portion of the git repo and pass the JSON report data through, I think it's still good to separate the report generation from the report display portions into separate jobs. Though we don't do it here, we could imagine some post processing taking place for presentation and that can be done in the display portion (ClinVarReportHTML here).

A sample run with a pipeline using a test VCF file and using the above two GitHub repos can be found at:

https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-0fq6djbem3pcrvo#Components

I won't link to it here but the pipeline has also been run with the other test data we've been given.

Copied from the review task:

Review code and pipeline:

• https://github.com/abeconnelly/ClinVarReport
• https://github.com/abeconnelly/ClinVarReportHTML
• https://workbench.su92l.arvadosapi.com/pipeline_templates/su92l-p5p6p-oopbp7ikcycckcw

Sample run:

• https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-0fq6djbem3pcrvo

Based on feedback from #8700, I've added a spinner to the ClinVar report as well.

The following sample run should have the updated changes:

• https://workbench.su92l.arvadosapi.com/collections/42de9014c53b5487c069a5b86909afc8+1911/clinvar-report.html

Thanks for addressing that. This looks good to go for me.