Chris Fields wrote, On 07/29/2011 12:35 PM:
On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
Question for galaxy maintainers: have you encountered situations where BWA jobs run 'forever' (for days) ? ... I'm wondering if this is common enough to justify adding "-A" to the wrapper, or is it rare enough and can be ignored.
Can it be added as an optional argument? So that if it is selected, the setting is passed to the tool, otherwise not.
Obviously, it can be added to the XML wrapper.
I'm asking if other people encountered this situation with Paired-end mapping, and whether it's rare or not.
From a user's perspective, this kind of parameter makes no sense:
it basically tells the user: "run BWA without this parameter, and if after 24 hours the job is still running, kill it and re-run with this parameter". That's not the way to build user-friendly tools :(
-gordon