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throw error when several bam files match possibleTumorSampleNamePrefixes set #29

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GWarsow opened this issue Feb 19, 2019 · 0 comments

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@GWarsow
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GWarsow commented Feb 19, 2019

assume to have xml file with

<cvalue name='possibleTumorSampleNamePrefixes' value='( metastasis tumor tumor02 tumor04 )' type='bashArray'/>

and the following bam files:

metastasis_PID_merged.mdup.bam
tumor_PID_merged.mdup.bam

Currently, metastasis is chosen as the tumor sample (tumor sample is simply neglected).
No warning/error is thrown to inform the user that several matching tumor bam files exist in the alignment folder.

Request: Throw an error (do not start worklow) and propose to set command line cvalue possibleTumorSampleNamePrefixes in order to explicitly choose one of both bam files.

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