Main branch not recognised when executing an online workflow

[marcodelapierre]

I have a github repo whose primary branch is called main instead of master, which is becoming increasingly common.
Nextflow asks me to specify the branch with -r :

$ nextflow run marcodelapierre/toy-cowsay-nf -profile condawave

N E X T F L O W  ~  version 22.12.0-edge
Pulling marcodelapierre/toy-cowsay-nf ...
 downloaded from https://github.com/marcodelapierre/toy-cowsay-nf.git
Project `marcodelapierre/toy-cowsay-nf` is currently stickied on revision: main -- you need to explicitly specify a revision with the option `-r` in order to use it

All good with -r:

$ nextflow run -r main marcodelapierre/toy-cowsay-nf -profile condawave

N E X T F L O W  ~  version 22.12.0-edge
Launching `https://github.com/marcodelapierre/toy-cowsay-nf` [cranky_hypatia] DSL2 - revision: cd804ac170 [main]
executor >  local (8)
[b7/d27846] process > sayHello (1) [100%] 4 of 4 ✔
[35/cabd24] process > cowSay (4)   [100%] 4 of 4 ✔

I suggest to enable Nextflow to look for both master and main branches.

[stale]

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.

[marcodelapierre]

pinging this one back as I think it should be discussed - should be a quick fix, if approved for action

@pditommaso @bentsherman @jordeu

[bentsherman]

Basically the AssetManager should be modified to accept both master and main as "default branch" names:

nextflow/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy

Lines 911 to 915 in fe5bea9

	if( current != defaultBranch ) {
	if( !revision ) {
	throw new AbortOperationException("Project `$project` is currently stickied on revision: $current -- you need to explicitly specify a revision with the option `-r` in order to use it")
	}
	}

[marcodelapierre]

is there a way to know what is the default branch of a repo?

[jordeu]

is there a way to know what is the default branch of a repo?

The default branch concept do not exists on Git, it is a provider concept. I know that using Github API you can check which is the default branch.

[pditommaso]

Indeed https://stackoverflow.com/a/16501903/395921.

Very likely it's available also on BitBucket and GitLab

[ewels]

This just came up again, @BioWilko was asking if it was the case. I had totally forgotten about this issue and assured him that master couldn't be hardcoded in the codebase 👀 (then I tried it myself)

We're hoping to move to using main as the default branch name for all @nf-core repos soon, but will need to wait for this to be resolved first.

Is it solved by #4659?

[marcodelapierre]

Hey Phil, yep, at the moment any Nextflow git repo whose default branch is not master should have it explicitly mentioned in the manifest for proper functionality:

manifest {
  ..
  name = 'hello world'
  description = 'Toy pipeline for simple Nextflow tests'
  homePage = ' ... '
  ..
  defaultBranch = 'main'
  ..
}

The most developed open PR to handle multiple git revisions is #5089.
With it, pipelines with non master default branch will not give an error.
However, there is still a corner case caveat (documented in the PR) where the default branch appears duplicated in the list of branches, both as DEFAULT (or similar) and <defaultBranch name>. This happens if the pipeline has previously been called both with no -r/--revision flag AND with -r <defaultBranch name>. These two ways of calling the default branch may point to distinct commits over time; they can be reconciled by updating both to latest.

[ewels]

Possible approach to using git to figure this out here: https://stackoverflow.com/questions/28666357/how-to-get-default-git-branch

[ewels]

https://github.com/nextflow-io/socks now has default branch main, can use this for testing.

[pditommaso]

Smell bad 😆

[bentsherman]

Resolved by #5375