Project currently is stuck on revision xxx when using -latest flag

[marcadella]

Bug report

I get the error message: Project xxx currently is sticked on revision: yyy -- you need to specify explicitly a revision with the option -r to use it, even though I am using the -latest flag when running nextflow run.

There is no reason why Nextflow would not pull the latest commit of the master branch and use it when -r has been used previously.

Environment

• Nextflow version: 20.04.1.5335
• Java version: 11.0.7
• Operating system: Linux

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[thorellk]

I get this error message as well when running NEXTFLOW version 20.10.0 on our Linux HPC.

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[esrice]

I am having this issue as well. Should the default behavior in the absence of any flags not be to use the latest version of the default branch on github? Pulling a repository for the first time, these two commands:

nextflow run WarrenLab/longread-polish-nf [pipeline-specific parameters]
nextflow run WarrenLab/longread-polish-nf -latest [pipeline-specific parameters]

both crash with the error:

N E X T F L O W  ~  version 20.10.0
Pulling WarrenLab/longread-polish-nf ...
downloaded from https://github.com/WarrenLab/longread-polish-nf.git
Project `WarrenLab/longread-polish-nf` currently is sticked on revision: main -- you need to specify explicitly a revision with the option `-r` to use it

Whereas adding the flag -r main works. Should it look for a 'main' or 'master' branch by default? Is this perhaps an issue with github switching from using 'master' to 'main' as the default branch name?

[wbazant]

I've had this problem when pulling my own pipeline, which only has one branch and I didn't mind what I named it. Could 'main' be an okay default for pulling?

Being "sticked on revision" isn't even correct English but amazingly it helped me find this issue!

[krokicki]

I'm running into this issue on tower.nf, with the "pull latest" option set. I suspect that @esrice is correct that it has to do with the new 'main' branch, since I only have this issue with newer repos and not any that use 'master'.

[esrice]

@krokicki I looked into this more after writing that comment, and IIRC it is indeed an issue with 'master' being hard-coded into some code somewhere. I don't know enough groovy to write an elegant solution for this myself. However, I get around this in my own projects by either doing '-latest -r main' on the command line, or by adding this line to nextflow.config:

manifest.defaultBranch = 'main'

Hope this helps!

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This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.