Tapestry

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:

• https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-z9qiho889d52uid
• https://workbench.su92l.arvadosapi.com/collections/e1fa7630e0762d1b22090fda681b827a+1882/get-evidence-report.html

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

• https://workbench.su92l.arvadosapi.com/pipeline_instances/su92l-d1hrv-nhin4h27bqzjyvf
• https://workbench.su92l.arvadosapi.com/collections/2b4703eb27aeb44eaaa320ae1ec67669+1925/get-evidence-report.html

The pipeline template is su92l-p5p6p-2hdis7roemcaokr

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

• https://github.com/abeconnelly/GETEvidenceReport
• https://github.com/abeconnelly/GETEvidenceReportRefresh
• https://github.com/abeconnelly/GETEvidenceReportHTML

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.