Question for galaxy maintainers: have you encountered situations where BWA jobs
run 'forever' (for days) ?
A little digging shows that it's the "bwa sampe" step, and SEQanswers thread
mention it's somewhat common:
One suggested work-around is to add "-A" to "bwa sampe", but there's no way to
do it in the current BWA wrapper.
(On the command-line with the same input files it does make things much faster).
I'm wondering if this is common enough to justify adding "-A" to the wrapper,
or is it rare enough and can be ignored.
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