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AlexsLemonade / scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
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Add troubleshooting section to external instructions #690

Open sjspielman opened 6 months ago

sjspielman commented 6 months ago

Also, it seems that the workflow always wants the -r version flag. If you try to run without one, it fails with the error:

Project `AlexsLemonade/scpca-nf` is currently stickied on revision: v0.7.2 -- you need to explicitly specify a revision with the option `-r` in order to use it

This error is not an always error. It has to do with what the last pulled version was. If you run nextflow pull without -r you should get the latest version and then be able to run it just fine. Which is to say that -r is not always required, but it is a often good idea.

Rather than adding -r everywhere, maybe we add a "troubleshooting" section? I would say if you see that error, try nextflow pull AlexsLemonade/scpca-nf to get the latest release, then try again. In general, I would rather have external users use the latest version unless they have a reason to stick with an old one.

Originally posted by @jashapiro in https://github.com/AlexsLemonade/scpca-nf/issues/688#issuecomment-1930626095

As quoted above, we may want a troubleshooting section which includes the "error" that users may encounter if they don't provide -r.

allyhawkins commented 6 months ago

Just noting this original issue here. Although I don't know if any of the things from the original issue really need to be addressed anymore so I'm going to close the old one.

allyhawkins commented 6 months ago

Maybe switching between docker and singularity would be the most helpful from that list.

sjspielman commented 6 months ago

🎢 from #690, just in case...

Some ideas to include right now would be:

  • how to clear the nextflow cache for the repo if trying to run an updated version
  • how to change the name of the queue used for your job scheduler (some places call it partition)
  • how to switch between docker and singularity