feat: return collection for SANGER_READ_RUN workflow parameter variable (#468)

[hunterckx]

Closes #468

Based on main as opposed to (as suggested in the ticket) fran/456-paired-end-step because the latter has linting errors which would make things awkward

[hunterckx]

Thanks for the feedback @mvdbeek! I've updated it to use the run accession, and opened this for review -- could you take a look?

One thing I want to note is that I've set it up to use the file with _1 in the name for the "forward" data, and the file with _2 for the "reverse" data, which I don't actually know for sure is accurate. Any insight on that?

[NoopDog]

Hi @mvdbeek can you take a look at @hunterckx's questions above? Thanks! D

[mvdbeek]

I've updated it to use the run accession, and opened this for review -- could you take a look?

Thanks, yes, that looks good.

One thing I want to note is that I've set it up to use the file with _1 in the name for the "forward" data, and the file with _2 for the "reverse" data, which I don't actually know for sure is accurate. Any insight on that?

Not really, since the ; is what the ENA API serves I would assume they provide the files in the correct order, so what I would do is just accept that order instead of guessing using the _1 / _2 heuristic. We have some contacts to the ENA (@bgruening @wm75 do you know anyone we can contact about this question ?), the best option I guess is to clarify this.
The second best is to sample a large number of paired runs and see if the _1 / _2 heuristic holds up ?

[hunterckx]

Cool -- I'll go ahead and merge this and we can address forward/reverse determination in a separate ticket: #471