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nf-core
Documentation for stub running
Is your feature request related to a problem? Please describe
In the cases where tests absolutely require too large files, there is functionality for running as stub. However this needs more documentation (as suggested by @drpatelh).
Describe the solution you'd like
It would be nice with a short tutorial, including clear guidelines for when stub-running is ok and when it is not. Additionally it could - on a more long term - be nice if this was included as nf-core scripting functionality, but I think for now just some text along with example modules would suffice.
Describe alternatives you've considered
It's possible to make stub-running already once one knows which modules to look at. Phyloflash by @ramprasadn is a good example.
Additional context
Maybe it'd be a good idea for the upcoming hackaton?
intriguing name this! sounds a bit like a subversive sort of unit-testing! So it's not OK sometimes then? I had a look at phyloflash a did a simple "nextflow run main.nf" but was told no enworkflow was available. I've done a google searhc to and nothing has come up either.
Hi @rafalcode do you wanna work together on this? I was thinking to look into it sometime soon. I'm in the (virtual) cafe on gather-town. I think overall the idea is something like 'in case all other unit testing fails because of requirement for too big files"
Hi @lassefolkersen, yes that could be a good idea. I was in gather-town this morning, but I have a bit of workload today, so I can only pop in now and then. Tomorrow I'm going to have more spare time.
Ok - maybe I just do the writing and stuff, I was planning to anyway, and then list you as reviewer. Would appreciate a second set of eyes on it.
Hi, we are also some local modules for the new proteinfold pipeline, still a draft though, that would need to incorporate the stub-run option so I will be happy to take a look at the PR or help if I can.
Hi @rafalcode I made a pull request now. Couldn't put you as reviewer, I think maybe it's just the nf-core team. But here's the link 😄
@mribeirodantas This is closed by https://github.com/nf-core/website/pull/1079, no?
I will close this now, but feel free to reopen if the linked PR did not solve it :)