Only Github repo ?

[Raynooo]

Hi,
We are currently working on integrating a bunch of tools in Galaxy and want to package them so they are quick installed and deployed. It seems your repo for Flash is the only one on github and is more up-to-date than the sourceforge one.
Does your version (which seems to be 1.2.11 according to the README) significantly differs from the one on sourceforge ? Would you reckon that a workflow configured for the legacy 1.2.11 also works with yours ?

[msettles]

Hello Raynooo, the version here is meant to augment the FLASH version on sourceforge. It does have slightly different behaviors particularly for "outie overlaps", the original leaves on the adapter sequence, whereas FLASH2 removes them, allows for different length reads and removes excessively low quality reads (ala adapter dimers)

[Raynooo]

Hi,
Thanks for your quick answer. Since I'm only packaging the stuff and not actually using it, I'll use the old sourceforge right now but I'll make sure to warn potential users that your version might interest them more.
Cheers !