nextflow pull -r needs to be run twice to pull remote tag

[SamStudio8]

Bug report

Expected behavior

nextflow pull -r <tag> checks out a new tag from the remote repository.

Actual behavior

• nextflow pull -r <tag> yields the following error: Cannot find revision <tag> -- Make sure that it exists in the remote repository
• A second nextflow pull -r <tag> is successful

Steps to reproduce the problem

# Check out a known past tag
nextflow pull -r v1.0.0 epi2me-labs/wf-basecalling
LOCAL_PATH=$(nextflow info epi2me-labs/wf-basecalling | grep 'local path' | sed -nE 's, local path  : (.*),\1,p')
cd ${LOCAL_PATH}
# Nuke a known "future" tag
git tag -d v1.0.1
# Try and check it out with nextflow pull
nextflow pull -r v1.0.1 epi2me-labs/wf-basecalling
# check out again, successfully
nextflow pull -r v1.0.1 epi2me-labs/wf-basecalling

Environment

• Nextflow version: 23.04.2
• Java version: OpenJDK 64-Bit Server VM Homebrew (build 17.0.3+0, mixed mode, sharing)
• Operating system: macOS
• Bash version: zsh 5.8 (x86_64-apple-darwin21.0)

Additional context

Running Nextflow pull on an existing asset repo, triggers the following events:

• AssetManager.download
• git.checkout() .setName(revision) .call(), which will fail because the repository has not been fetched yet
• checkoutRemoteBranch(revision), triggered by the failure of the first git.checkout()
• fetch.call(), where the remote repository is now fetched
• A second and fatal git.checkout(), which fails because it tries to specifically track an upstream origin/<revision> branch (but revision is a tag)

When running the command a second time, the repository is successfully updated by the first git.checkout().setName(revision).

Some initial thoughts on how to work around this:

• the repository should always be fetched before attempting the first git.checkout().setName(revision), or
• after failing to track a branch in checkoutRemoteBranch, download could attempt to checkout the revision as a tag

[SamStudio8]

Hey @bentsherman, thanks for the patch on this. Is there a plan to merge 4247?

[bentsherman]

Just waiting for @pditommaso to approve

[SamStudio8]

@pditommaso

[pditommaso]

I was testing the associated PR, however I was not able to replicate the reported issue. This command works for me

» nextflow pull -r v1.0.1 epi2me-labs/wf-basecalling
Checking epi2me-labs/wf-basecalling ...
 downloaded from https://github.com/epi2me-labs/wf-basecalling.git - revision: 3047f23c74 [v1.0.1]

What am I missing?

[bentsherman]

You have to delete the tag from the git repo to force git to pull a remote tag separate from the initial clone, like pulling a new release. See the "steps to reproduce the problem" in the OP