Discussion: maybe not use latest as the defaultBranch?

[jashapiro]

In trying to test the latest updates, I ran into an interesting little situation where Nextflow was not behaving quite as I expected it to.

I wanted to test the first run experience for users, so I ran nextflow drop alexslemonade/scpca-nf to clear the downloaded workflow cache.

Next I tried to run nextflow run alexslemonade/scpca-nf, which resulted in the following error:

Project `alexslemonade/scpca-nf` currently is sticked on revision: main -- you need to specify explicitly a revision with the option `-r` to use it

The cause of this error seems to be that nextflow only pulls the GitHub default branch, so the latest branch was not present, and thus it could not find it to run.

Using nextflow run alexslemonade/scpca-nf -r latest does work, and subsequent runs work as expected, with no need to specify the revision.

So I thought there might be a couple options:

• We could update our instructions to specify the -r latest flag, but a hope was that we could eliminate that flag for easier running.
• Alternatively, we could tell people to run nextflow pull alexslemonade/scpca-nf -r latest as a first step, which should then allow them to use bare nextflow run alexslemonade/scpca-nf when running the workflow.
• We could switch the manifest.defaultBranch to main, which should allow for the bare nextflow run alexslemonade/scpca-nf to work without a mysterious error. In this case, I think we would want to create a separate dev branch to use as we add features, merging usually to that branch and then from dev into main when we are preparing a release.

(My ideal solution would probably be for Nextflow to automatically pull whatever is specified in the manifest.defaultBranch, but judging by the age of this issue, I am not optimistic for a quick fix on that front. I think the expectation is that manifest.defaultBranch is matching the GitHub default branch. )

[jashapiro]

Tagging @allyhawkins & @jaclyn-taroni for comment.

[allyhawkins]

We could switch the manifest.defaultBranch to main, which should allow for the bare nextflow run alexslemonade/scpca-nf to work without a mysterious error. In this case, I think we would want to create a separate dev branch to use as we add features, merging usually to that branch and then from dev into main when we are preparing a release.

I'm tempted to go with this option. It seems the most straight forward for users and also would work well for us. The other options are not impossible to get around, but seem more error prone for users.

[jaclyn-taroni]

We could switch the manifest.defaultBranch to main, which should allow for the bare nextflow run alexslemonade/scpca-nf to work without a mysterious error. In this case, I think we would want to create a separate dev branch to use as we add features, merging usually to that branch and then from dev into main when we are preparing a release.

I'm tempted to go with this option. It seems the most straight forward for users and also would work well for us. The other options are not impossible to get around, but seem more error prone for users.

Agreed.

[jashapiro]

Okay! Sounds good to me. I will work on setting that up, including some updated instructions.

[allaway]

Just hopping in to say thank you for documenting this; I am running into this issue and this thread was very helpful!