Task #8859

Feature #8700: Arvados job/pipeline generates GET-Evidence HTML report from VCF

Review #8700

Added by Abram Connelly almost 4 years ago. Updated almost 4 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Start date:
03/30/2016
Due date:
% Done:

0%

Estimated time:

Description

The GET-Evidence pipeline is producing HTML reports for VCF and non-VCF (e.g. CGI-Var) data files.

An example run with a data file that was converted to VCF from 23andMe:

An example run with a date file that was originally a CGI-Var file:

The pipeline template is su92l-p5p6p-2hdis7roemcaokr

The three repositories for each leg of the pipeline can be found at:

This closely resembles how the pipeline was setup. The initial report is generated with GETEvidenceReport, then refreshed with the latest GET-Evidence database by running GETEvidenceReportRefresh. Finally, the HTML is created with GETEvidenceReportHTML. The major differences from the previous incarnation of the GET-Evidence pipeline from this one are that this one is able to injects VCF and create a report and the final report resides completely in Arvados, rather than the GET-Evidence server.

History

#1 Updated by Abram Connelly almost 4 years ago

  • Assigned To set to Ward Vandewege

#2 Updated by Ward Vandewege almost 4 years ago

  • Status changed from New to In Progress

#3 Updated by Ward Vandewege almost 4 years ago

  • Status changed from In Progress to Resolved
  • Remaining (hours) set to 0.0

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