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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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ORANGE (v2.5.0) could not find features plots from CUPPA (v1.8) #428

Closed YingYa closed 9 months ago

YingYa commented 1 year ago

I am running ORANGE (v2.5.0) to summarize the key outputs from all algorithms in the Hartwig suite.

But some samples failed to run when '-cuppa_feature_plot' was specified, because of the lack of features plot (tumor-id.cup.report.features.png) from CUPPA.

Base on the line 143 to line 191 of the source code CupGenerateReport_pipeline: samples with features less than 15 will only get a merge summary plot with features; samples with features more than 15 will get separated features plot and summary plot, but summary plot without features.

Could ORANGE return warning but not error, when run with parameter '-cuppa_feature_plot' but lack of features plot?

kduyvesteyn commented 10 months ago

Suggestion makes sense but suggest to switch to ORANGE 2.6.0 instead (although I see there is no proper release linked yet). In this version you only have to provide individual dirs, so you can provide cuppa_dir and ORANGE will determine whether there is a feature plot to be used or not.