make read structure argument optional instead of mandatory

Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs

MIT License

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make read structure argument optional instead of mandatory #7

Open Kurt-Hetrick opened 1 year ago

Kurt-Hetrick commented 1 year ago

parse RunParameters.xml by default unless end user specifies a specific value

Kurt-Hetrick commented 1 year ago

keeping read structure argument mandatory unless lab managers would like to try making it optional. Optional would mean that RunParameters.xml is parsed by default and assumptions are made to create READ_STRUCTURE. If that assumption is not valid then end user can submit demuxing pipeline specifying their own READ_STRUCTURE.