I have a production local version of galaxy running at our institution. After our illumina spits out the bcl files we run bcl2fastq and put it into our storage archive. What I want to be able to do is add these raw fastq.gz files as data libraries into galaxy without copying into galaxy. So far this works fine by mounting the storage archive in galaxy and adding the directories as datasets from filesystem paths.
The issue I've got is that bcl2fastq stores them as fastq.gz files and adding these as a data library in this way means that the autodetect file type assigns them as 'data'. I don't really want galaxy to attempt to uncompress anything like it does if you do a standard upload, and a lot of tools can work with fastq.gz files (e.g. fastqc and trinity). However since the files are assigned as format 'data', nothing works with them and there is no fastq.gz file type in the datatypes_conf.xml.
Has anyone dealt with a similar issue with working with fastq.gz's in data libraries or have any advice how to integrate these more easily?