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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Balsamic ascatNgs PDF report available in Scout #3050

Closed ivadym closed 2 years ago

ivadym commented 2 years ago

Feature

Adapt Scout to display the BALSAMIC generated ascatNgs PDF report for tumor-normal WGS analyses, which contains the main ascatNgs output plots, as well as a table with some sample statistics.

The generated file has the following structure: CNV.somatic.TN_WGS.ascat.output.pdf

Context

HK tags: ascatngs, visualization Balsamic tags: ascat-output-pdf, research-ascat-output-pdf

Related issue in BALSAMIC: https://github.com/Clinical-Genomics/BALSAMIC/issues/827 Hermes PR: https://github.com/Clinical-Genomics/hermes/pull/45

northwestwitch commented 2 years ago

Hi @ivadym, what's the status of this in cg? Is there a specific key added to the Scout case config file that I can use to link the file to a cancer case?

northwestwitch commented 2 years ago

I'm asking because Scout already supports the loading of a CNV report, check the demo instance.

image

The key used in scout to load a generic CNV report is cnv_report check an example of a demo file : https://github.com/Clinical-Genomics/scout/blob/e972e88c08c1991b55c4e8f0087b0ec254abba2b/scout/demo/cancer.load_config.yaml#L43

Perhaps it can be used to load ascat reports via CG?

ivadym commented 2 years ago

It was supposed to be used to load a CNVkit output report, but since this PDF is not finally delivered, I think we can reuse the cnv_report key for this cause.

northwestwitch commented 2 years ago

Closing this, as the key has been named cnv_report in the cancer case config file: https://github.com/Clinical-Genomics/cg/pull/1384#event-6034151676