split_libraries_fasetq should have a ADDED_DEMULTIPLEX_FIELD

[ElDeveloper]

split_libraries.py has the -j option which allows you to deal with duplicated barcodes across different "runs/lanes", however split_libraries_fastq.py does not include this option.

One of the things to note is that once this is changed (if it's changed), the Illumina tutorial should be updated to include the new field in the mapping file and in turn not requiring multiple mapping files and an additional merging step.

[gregcaporaso]

This is supported by passing multiple input and mapping files, as illustrated in the split_libraries_fastq of the Illumina Overview Tutorial. I think we should leave that as-is for now as there are a lot more pressing things to work on, since this has worked well so far. Closing this for now, but re-open with a comment if there are compelling use cases. I think we really want to avoid having a really complicated interface like we do for split_libraries.py.

[ElDeveloper]

The reason why I opened this issue is because we are working on figuring out the pipelines that we will be using for http://github.com/qiime/QiiTa-ware and the RUN_PREFIX field is and will continue to be a required field in every prep template, hence this is a feature that we decided we needed.

@wasade, @antgonza or @adamrp did I miss something here?

[antgonza]

AFAIK no.