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Catch error during final report rendering when refgene and cpgislandfile are not given #184

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alexg9010 opened this issue Aug 10, 2022 · 0 comments

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alexg9010 commented Aug 10, 2022

settings:

[..]
   differential-methylation:
     cores: 1
     qvalue: 0.01
     difference: 25
     annotation:
       cpgIsland-bedfile: ''
       refGenes-bedfile: ''
       # download cpgIsland-bedfile or refGenes-bedfile automatically if not given?
       webfetch:   no
[..]

Error Log:

|.....................................................                 |  76%
Quitting from lines 289-296 (index.Rmd)
Error in lookupBedFile(type = "refGene", filename = refGenes_bedfile,  :
  ERROR: type can be either "cpgIslandExt" or "knownGene".
Calls: render2HTML ... eval_with_user_handlers -> eval -> eval -> lookupBedFile

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