Plugin version causes error in `nextflow plugin` command

[JosuaCarl]

Bug report

Expected behavior and actual behavior

When specifying a version the correct version should be loaded from a local repository.

Steps to reproduce the problem

Works (with the current version 1.2.1):

nextflow plugin nf-co2footprint:postRun --tracePath out/pipeline_info execution_trace.txt --config nextflow.config

Does not work:

nextflow plugin nf-co2footprint@1.2.1:postRun --tracePath out/pipeline_info execution_trace.txt --config nextflow.config

Program output

nextflow plugin nf-co2footprint@1.3.0:postRun --tracePath out/pipeline_info/execution_trace_2026-05-06_09-55-52.txt --config nextflow.config
->

nf-co2footprint plugin  ~  version 1.3.0
Cannot find target plugin: nf-co2footprint@1.3.0

The first line is from the plugin itself, showing that it is loaded and started. I could trace the path of the command being issued to the version and plugin name being correctly
parsed:

nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy

Lines 73 to 79 in ab6be6d

	final head = args.pop()
	final items = head.tokenize(CMD_SEP)
	final target = items[0]
	final cmd = items[1] ? items[1..-1].join(CMD_SEP) : null
	// push back the command as the first item
	Plugins.start(target)

, interpreted:

nextflow/modules/nf-commons/src/main/nextflow/plugin/PluginRef.groovy

Lines 47 to 55 in ab6be6d

	static PluginRef parse(String fqid, DefaultPlugins defaultPlugins=null) {
	final tokens = fqid.tokenize('@') as List<String>
	final id = tokens[0]
	final ver = tokens[1]
	if( ver || defaultPlugins==null )
	return new PluginRef(id, ver)
	if( defaultPlugins.hasPlugin(id) )
	return defaultPlugins.getPlugin(id)
	return new PluginRef(id)

,loaded:

nextflow/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy

Lines 223 to 228 in ab6be6d

	boolean installPlugin(String id, String version) {
	if( !pluginsStore )
	throw new IllegalStateException("Missing pluginStore attribute")
	return load0(id, version)
	}

with the intended path ($HOME/.nextflow/plugins/nf-co2footprint-1.3.0):

nextflow/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy

Line 383 in ab6be6d

PluginWrapper wrapper = pluginManager.loadPluginFromPath(pluginPath)

, and started (this is where the plugin first logs its version):

nextflow/modules/nf-commons/src/main/nextflow/plugin/PluginUpdater.groovy

Lines 414 to 415 in ab6be6d

	PluginState state = pluginManager.startPlugin(id)
	return PluginState.STARTED == state

However, after the successful startup the plugin can not be fetched from the manager and the wrapper is null, leading to the error:

nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy

Lines 80 to 82 in ab6be6d

	final wrapper = Plugins.manager.getPlugin(target)
	if( !wrapper )
	throw new AbortOperationException("Cannot find target plugin: $target")

Environment

• Nextflow version: 26.04.0
• Operating system: MacOS

Additional context

So my question is: Why does the plugin start up correctly, but is not found in the manager? And why does it work if I do not supply a specific version?

Relates to nextflow-io/nf-co2footprint#391

[JosuaCarl]

I think the solution is to change Plugins.manager.getPlugin(target) to Plugins.manager.getPlugin(pluginName)

beacuse target is nf-co2footprint@1.3.0, but the plugins Map in the AbstractPluginsManager from pf4j saves the entry under nf-co2footprint. This is also why it works, if no version is specified.

Could be done similar to the interpretation, like:

final List<String> targetSplit = target.tokenize('@') as List<String>
final String pluginName = targetSplit[1]
Plugins.manager.getPlugin(pluginName)