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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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[WARN ] - sample(tumor-id) missing viral annotations file #430

Closed YingYa closed 1 year ago

YingYa commented 1 year ago

I am running CUPPA (v1.8) with the warning: [WARN ] - sample(tumor-id) missing viral annotations file: /path/to/linx/tumor-id.virus.annotated.tsv

CUPPA will look up the viral annotations file in linxDataDir: https://github.com/hartwigmedical/hmftools/blob/2f15ed662f5f308a25e5694bb552fb15d1abb4a7/cuppa/src/main/java/com/hartwig/hmftools/cup/feature/FeatureDataLoader.java#L111

Should the viral annotations file in virusbreakend directory but not the linx directory?

p-priestley commented 1 year ago

Thanks for your multiple bug reports - we will look at these shortly.

Since you are using multiple different tools, I would be interested to understand your use case and which institution it is for so we can give better advice. Perhaps you could email me at p.priestley@hartwigmedicalfoundation.nl if you would like to discuss.

charlesshale commented 1 year ago

The virus interpreter needs to be moved into the Linx directory, otherwise use the config 'sample_data_dir' and put all applicable sample pipeline output files in there.