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Plugin did not take subcommand options #5084

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sfc-gh-hyu opened this issue Jun 20, 2024 · 3 comments · May be fixed by #5643
Open

Plugin did not take subcommand options #5084

sfc-gh-hyu opened this issue Jun 20, 2024 · 3 comments · May be fixed by #5643
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@tom-seqera
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plugins

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@sfc-gh-hyu
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I am trying to develop a plugin against nextflow, however, it seems that subcommand options is considered as a parent command options:

Here is a simple plugin:

class MyPlugin extends BasePlugin implements PluginAbstractExec{

    MyPlugin(PluginWrapper wrapper) {
        super(wrapper)
    }

    @Override
    List<String> getCommands() {
        [ 'run' ]
    }

    @Override
    int exec(String cmd, List<String> args) {
        System.out.println("command array: " + Arrays.toString(args))
        if( cmd == 'run' ) {
            return 0
        }
        else {
            System.err.println "Invalid command: ${cmd}"
            return 1
        }
    }
}

When I run the plugin

$ ./launch.sh plugin nf-foo:run
command array: [[]]
$ ./launch.sh plugin nf-foo:run --foo bar
Unknown option: --foo=bar -- Check the available commands and options and syntax with 'help'

Did I miss anything?
@sfc-gh-hyu
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Ping on this. Is there any plan to fix this?

@bentsherman
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@sfc-gh-hyu sorry for the delay, we will look into it when we have some time

@tom-seqera
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@sfc-gh-hyu my understanding is that anything prefixed by - or -- will currently be treated by nextflow as an option for nextflow itself. You can pass arguments to the plugin command without prefixes, like so:

$ ./launch.sh plugin nf-foo:run bar
command array: [[bar]]

$ ./launch.sh plugin nf-foo:run foo bar
command array: [[foo, bar]]

@jagedn jagedn linked a pull request Jan 6, 2025 that will close this issue
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@bentsherman bentsherman linked a pull request Jan 10, 2025 that will close this issue
allows parameters when run a plugin subcommand #5643
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@tom-seqera tom-seqera

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allows parameters when run a plugin subcommand jagedn/nextflow
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@bentsherman @sfc-gh-hyu @tom-seqera