Feature #8701

Arvados job/pipeline generates ClinVar HTML report from VCF

Added by Tom Clegg almost 4 years ago. Updated almost 4 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
Category:
-
Start date:
03/22/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
2.0

Subtasks

Task #8768: Review #8701ResolvedWard Vandewege

History

#1 Updated by Tom Clegg almost 4 years ago

  • Subject changed from Arvados job/pipeline generates ClinVar HTML report to Arvados job/pipeline generates ClinVar HTML report from VCF

#2 Updated by Ward Vandewege almost 4 years ago

  • Story points set to 2.0

#3 Updated by Ward Vandewege almost 4 years ago

  • Assigned To set to Abram Connelly

#4 Updated by Abram Connelly almost 4 years ago

  • Status changed from New to In Progress

I think the best way to go about this is to separate the pipeline into two jobs. The first will produce a JSON output file and the second will take the JSON file and create an HTML page. I guess we'll need to duplicate the report in the second job so it's available from the same collection?

The first leg of that pipeline is created and looks to be running successfully. I've based it off of Madeleine's vcf2clinvar. I've used abe.vcf from a project I've created called ClinVar that holds relevant data for this pipeline.

The pipeline is called ClinVar Report Pipeline. The test run ran successfully and produced a JSON 'report' as expected.

#5 Updated by Abram Connelly almost 4 years ago

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.

#6 Updated by Abram Connelly almost 4 years ago

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

Two GitHub repositories have been created:

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.

#8 Updated by Ward Vandewege almost 4 years ago

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

#9 Updated by Abram Connelly almost 4 years ago

  • Status changed from In Progress to Closed

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