Hi all,

I'm trying to work out how to use the groups of reads output option in the FASTQ and BWA Short Read Mapper component, and I have a couple of questions maybe someone can help me with:

1. If you use groups of reads as output, in the FASTQ reader you see the input file name but once you map using BWA you lose that original file name, you get only the temporary bam file name.  Is there any way to keep which fastq file the reads came from so they can be identified in the repository?  I want to load multiple fastq (paired) files, but each pair belongs to an individual sample that I want to be able to identify in the repository.  What would be the best way to load multiple files in this case?
2. When using groups of reads in the BWA mapper, only one batch is created per file (group) so only one process/thread is created per file.  Is this correct?  This means you cannot use parallel processing when the output is groups of reads.

Thanks,

Liz