You need to append it regardless of whether it's already in the list because there are some cases where you'd need to pass the same file multiple times. One example of that would be if you had two replicate HiSeq lanes, and were demultiplexing with ``split_libraries_fastq.py``. In that case you'd like pass the same mapping file twice, but different read and index fastq files. For example:

```
split_libraries_fastq.py -i lane1.fastq,lane2.fastq -b lane1_index.fastq,lane2_index.fastq -m universal_map.txt,universal_map.txt
```