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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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PDF report output #366

Closed davidvanzessen closed 1 year ago

davidvanzessen commented 1 year ago

Hello,

We've set up and are testing the targeted panel pipeline, for TSO500 data, in our department. Some of us have had a tour of the HMF facilities/software and we wondered if the PDF reports they were shown, that summarizes the result, were included in this pipeline output. I've done a search through the output files, but this report doesn't seem to be included.

Is it possible to generate this PDF report for this pipeline?

Hope it's clear what PDF we mean, I'm not sure what it's called and don't have an example :)

kduyvesteyn commented 1 year ago

The pipeline produces an ORANGE PDF and JSON file (https://github.com/hartwigmedical/hmftools/tree/master/orange) which may be what you are looking for. Current ORANGE version doesn't fully support panels yet but upcoming version will (v2.3, scheduled for end of week, probably pipeline v5.32).

The JSON file is meant to be starting point for downstream clients (eg we use ORANGE as starting point for https://github.com/hartwigmedical/actin).