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Update library parameter assignment in parameters.csv
The parameter list assumes that every new run is a new library preparation. This might cause artifacts not to be removed by MarkDuplicates. My suggestion is to make this parameter less greedy or track library preparations.
old:
runPrefix ${sequencingStartDate}_${sequencer}_${run}_${flowcell}
filePrefix ${runPrefix}_L${lane}
library ${filePrefix}
#parametric expansion results in:
library ${sequencingStartDate}_${sequencer}_${run}_${flowcell}_L${lane}
new:
#better
library ${externalSampleID}_${barcode}