Hi Dan,

Daniel Blankenberg wrote, On 03/29/2011 10:55 AM:
> When files are added to Galaxy, the datatype can be directly set to
> any of the fastq variants (e.g. fastqillumina), which removes the
> requirement of grooming (but should only be done when users know what
> they are doing).

I'm not using the "get data" tool, we have our own import tools (uploading huge 
files with HTTP is not stable enough for me).
You're right that I should change the format of this tool from 'fastq' to 
'fastqillumina' (but the tool pre-dated all those built-in formats in galaxy, 
so I never bothered to update it...).

> 
>> The one time I've tried to make the built-in Bowtie tool available,
>> I got complaints about "why isn't my FASTQ file appear in the input
>> list" - because it was "fastq" and not "fastqsanger" after grooming
>> - this is a silly technical step that should not be a concern to
>> users - so I'm taking it out of the equation here (not to mention
>> that grooming two 14GB FASTQ files for every lane is a huge waste
>> of space and time).

> It should not be possible to have a data.ext=='fastq' after Grooming
> (unless manually changed by a user), please report the steps that
> lead to this.

Sorry, I didn't explain myself correctly:
I forbid users from grooming anything (just joking, but I really really 
discourage its use) - so all the datasets are 'fastq' not 'fastqsanger'.
There is no bug - the groomer is simply not used.
As stated above, I should change the output format from 'fastq' to 
'fastqillumina' (but up until this recent changeset it wouldn't have made any 
different, because the bowtie tool would not have accepted fastqillumina).


-gordon
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