On Jan 28, 2011, at 2:38 AM, Steve Taylor wrote:

>> You'll need to groom the files to convert them from fastq format to 
>> fastqsanger format, which is the format accepted by Galaxy's NGS tools. See 
>> the FastqGroomer tool for details. (If you're confident your fastq quality 
>> scores are in Sanger format, you can simply change the fastq dataset's 
>> datatype by clicking on its pencil and looking for the datatype selection on 
>> the page. This will take less time than running the groomer.)
> Assuming you are confident of the fastq format, is there anyway to do this 
> non-interactively, so you can run bowtie directly on the fastq sequences 
> without using FastqGroomer (for example, in a Workflow)?

One option for handling this within workflows is to add a "Change Datatype" 
action to the previous step with the fastq file, and set it to fastqsanger that 
way.  This doesn't manipulate the dataset at all or try to do any conversion, 
it just changes the datatype.

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