Is it possible to use looper link on a generic pipeline?

[nsheff]

The docs say looper link requires pipestat to be set up.

The thing is, I don't think it should require pipestat... as long as there's an output schema, I think I should be able to use looper link.

Use case:

I have a simple pipeline interface to run cellranger-atac across samples:

sample_interface:
  command_template: >
    cellranger-arc count \
      --id={sample.sample_name} \
      --reference={project.refpath} \
      --libraries="{looper.piface_dir}/{sample.library_sheet}" \
      --localcores={compute.cores} \
      --localmem={compute.mem}

nothing complicated. the pipeline is not made by me, it's using a general third-party tool. So, obviously it doesn't use pipestat.

I feel I should now be able to:

1. create an output schema that describes the outputs of this pipeline.
2. attach that output schema somewhere
3. run looper link

Maybe you can do this but I couldn't find any documentation about it:

https://pep.databio.org/looper/how-to/link-objects/

Here it says:

You must configure pipestat to use this feature.

Here it doesn't discuss it, as this tutorial is really focused on using pipestat to report results:

https://pep.databio.org/looper/user-tutorial/user-pipestat/

I suggest:

• Add a bit about how looper link works to the pipestat user tutotiral
• Increase docs on the looper link page
• allow it to work with just an output schema

[donaldcampbelljr]

I double checked this and found that we are requiring a pipestat backend to use the link functionality. looper link calls pipestat link which retrieves results objects with paths, groups them together by type and then links them. It needs to know the path of the result so that it can create a sym link which is why we require access to the results backend. I guess you could give it an output schema and the parent results folder via looper and have it crawl the directory looking similar file types and then linking them. Though, at that point, do you even need the output schema to achieve this functionality?