[Amplicon Illumina] Issue with datasets that have multiple assays of the same target

[jihanyehia]

When running the pipeline from the DEV_Amplicon_Illumina_NF_conversion branch using datasets with multiple assays for the same target (ex. OSD-417), it is failing to create a runsheet (at GET_RUNSHEET process) with the following error:

In addition, the --specify-runsheet argument cannot be passed to the pipeline as it is not part of the pipeline's declared parameters.