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nextflow plugins -help: show subcommands #7197

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34d5eb1
nextflow plugins -help: show subcommands
ewels Jun 2, 2026
7d894ce
Merge branch 'master' into subcommand-help
pditommaso Jun 5, 2026
81db3ae
nextflow plugin -help: handle colon form and show usage on error
ewels Jun 6, 2026
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57 changes: 54 additions & 3 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdPlugin.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ import org.eclipse.jgit.api.Git
*/
@CompileStatic
@Parameters(commandDescription = "Execute plugin-specific commands")
class CmdPlugin extends CmdBase {
class CmdPlugin extends CmdBase implements UsageAware {

@Override
String getName() {
Expand All @@ -51,10 +51,61 @@ class CmdPlugin extends CmdBase {
@Parameter(names = ['-template'], description = 'Plugin template version to use', hidden = true)
String templateVersion = 'v0.3.0'

/**
* Print the command usage help
*/
@Override
void usage() {
usage(args)
}

/**
* Print the command usage help
*
* @param args The arguments as entered by the user
*/
@Override
void usage(List<String> args) {
List<String> result = []
if( !args ) {
result << this.getClass().getAnnotation(Parameters).commandDescription()
result << 'Usage: nextflow plugin <sub-command> [options]'
result << ''
result << 'Commands:'
result << ' install <pluginId,...> Install a plugin'
result << ' create [<name> <provider> [dir]] Create a new plugin project from the template'
result << ' <plugin-name>:<command> [args] Execute a plugin-specific command'
result << ''
result << 'See the documentation of an individual plugin for its plugin-specific commands.'
result << ''
}
else {
switch( args[0] ) {
case 'install':
result << 'Install a plugin'
result << 'Usage: nextflow plugin install <pluginId,...>'
result << ''
break
case 'create':
result << 'Create a new plugin project from the official template'
result << 'Usage: nextflow plugin create [<plugin name> <provider name> [project path]]'
result << ''
result << 'When no arguments are provided, the command prompts interactively for the required values.'
result << ''
break
default:
throw new AbortOperationException("Unknown plugin sub-command: ${args[0]}")
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@pditommaso pditommaso Jun 6, 2026

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The default branch aborts on the <plugin-name>:<command> form, which is the third invocation advertised in the top-level help just above (and arguably the primary purpose of nextflow plugin).

For example nextflow plugin nf-hello:greet -help parses args = ['nf-hello:greet'], command.help is set, so Launcher.checkForHelp() calls usage() → usage(args). args[0] is neither install nor create, so this default throws Unknown plugin sub-command: nf-hello:greet — i.e. asking for help on a documented, valid invocation produces an error claiming it does not exist. (Execution in run() is fine — it handles the : form via args[0].contains(CMD_SEP); only the usage path aborts.)

Suggest falling back to general usage for the : form rather than aborting:

default:
    if( args[0].contains(CMD_SEP) ) {
        result << 'Execute a plugin-specific command'
        result << 'Usage: nextflow plugin <plugin-name>:<command> [args]'
        result << ''
        result << 'See the documentation of the individual plugin for its available commands.'
        result << ''
    }
    else {
        throw new AbortOperationException("Unknown plugin sub-command: ${args[0]}")
    }

This keeps the genuine typo error (e.g. nextflow plugin instal -help) while not blowing up on the legitimate plugin-command form. Worth a test pinning the behavior down.

}
}
println result.join('\n').toString()
}

@Override
void run() {
if( !args )
throw new AbortOperationException("Missing plugin command - usage: nextflow plugin install <pluginId,..>")
if( !args ) {
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@jorgee jorgee Jun 3, 2026

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I think we should print the reason of the failure before printing the usage

usage()
return
}
// setup plugins system
Plugins.init()
Runtime.addShutdownHook((it)-> Plugins.stop())
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