metaSpades only does co-assembly on collections

[jorondo1]

Hi,

I've been trying to pass a paired collection of samples to metaSpades, and cannot figure out how not to get a co-assembly. It seems as if by default, all samples are co-assembled and the only way to assemble samples separately is to call metaspades once per sample, which is not very practical with a few dozen samples.

I would have expected the collection mode to be a batch mode by default, triggering one job per pair. This is what MEGAHIT does on galaxy, with the option to switch on co-assembly if one wants to pool all samples.

Given that co-assembly is a very specific type of assembly that most people don't do because it doesn't always make biological sense, would it be possible to

• enable batch mode with collections
• make an optional co-assembly switch
  ?

Thank you

[bernt-matthias]

The solution is described here: #4658 (comment)

[jorondo1]

Thanks a lot! I looked for it through the issues, but not hard enough apparently. Cheers,

[bgruening]

@jorondo1 if you like please try to improve the help text of the tool,.so we help other users.

[bernt-matthias]

In addition the docs should be integrated in galaxy galaxyproject/training-material#6199 (comment)