Offline mode (NXF_OFFLINE='true') prevents running pipelines from local file:/ bare Git repositories

[nz-mtra]

Bug report

Expected behavior and actual behavior

When attempting to run a Nextflow pipeline using a local bare Git repository specified with the file:/ prefix (e.g., file:/path/to/my/pipeline.git), enabling offline mode with NXF_OFFLINE='true' causes Nextflow to fail prematurely. It throws an AbortOperationException stating that automatic downloads are disabled, even though the target is a local path that doesn't require remote downloading.

Expected behavior

Nextflow should recognize file:/ as a local resource, bypass the remote download check associated with being offline, and proceed to use the AssetManager to set up and run the pipeline from the specified local bare Git repository path.

Actual behavior

An AbortOperationException is thrown with a message similar to:
Unknown project 'local/pipelineName' -- NOTE: automatic download from remote repositories is disabled

Steps to reproduce the problem

1. Make a clean installation of nextflow.
2. Set NXF_OFFLINE variable to true (export NXF_OFFLINE='true')
3. Download a bare git repo of a pipeline. (git clone [email protected]:nf-core/rnaseq.git --bare)
4. Run the pipeline: nextflow run 'file:/path/to/local_pipelines/rnaseq.git' -r 3.18.0 -profile test

Program output

 N E X T F L O W   ~  version 24.10.6

Unknown project `local/rnaseq` -- NOTE: automatic download from remote repositories is disabled

.nextflow.log

Environment

• Nextflow version: 24.10.6
• Java version: openjdk - 17.0.14
• Operating system: linux
• Bash version: GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)

Additional context

Reproducibility seems to depend on the .nextflow.

This issue is on line 588 of nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy.
The AssetManager component is capable of handling these file:/ URIs correctly, but the current offline check blocks this unnecessarily.

Running the same local bare Git pipeline with NXF_OFFLINE='false' works even though the server does not have internet.