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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: