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When multiple adapters are given on the command line, they are first grouped by type and then searched in this order: 5', 3', anywhere. This behavior should be changed such that adapters are searched in the same order as they are provided on the command line, irrespective of type.
The actual order used for adapter trimming can be seen in the report. Currently, even if the command line contains
The order is relevant and can sometimes lead to different results. For example, trimming the read
This should be changed such that the