问Nextflow中的错误nextflow.cli.Launcher -@未知
EN

Stack Overflow用户

提问于 2022-10-02 03:55:37

回答 1查看 80关注 0票数 1

我刚刚开始学习nextflow，我遇到了一个奇怪的错误，我寻求一些指导。

这是我的密码

#!/usr/bin/env nextflow  
// Example1 from https://gist.github.com/elowy01/e9995d7ee8d6305930f868a10aeabbe9


params.str = 'Hello world!'

process AFcalc {

    """
    echo  '${params.str}'
    """
}

//this is necessary to print the output
result.subscribe {
    println it.trim()
}

当我运行代码时

nextflow run example1.nf

我犯了以下错误：

N E X T F L O W  ~  version 22.04.5
Launching `example1.nf` [nostalgic_brahmagupta] DSL2 - revision: 17976728a8
No such variable: result
 -- Check script 'example1.nf' at line: 15 or see '.nextflow.log' file for more details

当我看着

less .nextflow.log

我看到了这个

Oct-02 13:51:35.370 [main] DEBUG nextflow.cli.Launcher - $> nextflow run example1.nf
Oct-02 13:51:35.413 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.04.5
Oct-02 13:51:35.446 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Oct-02 13:51:35.460 [main] INFO  nextflow.cli.CmdRun - Launching `example1.nf` [nostalgic_brahmagupta] DSL2 - revision: 17976728a8
Oct-02 13:51:35.468 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/Users/theodosiou/.nextflow/plugins; core-plugins: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0
Oct-02 13:51:35.469 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Oct-02 13:51:35.474 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Oct-02 13:51:35.474 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Oct-02 13:51:35.476 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Oct-02 13:51:35.481 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Oct-02 13:51:35.511 [main] DEBUG nextflow.Session - Session uuid: ef770a53-e834-4fcd-8ae5-6216009b4ebc
Oct-02 13:51:35.511 [main] DEBUG nextflow.Session - Run name: nostalgic_brahmagupta
Oct-02 13:51:35.512 [main] DEBUG nextflow.Session - Executor pool size: 8
Oct-02 13:51:35.831 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.04.5 build 5708
  Created: 15-07-2022 16:09 UTC (18:09 CEST)
  System: Mac OS X 12.6
  Runtime: Groovy 3.0.10 on Java HotSpot(TM) 64-Bit Server VM 17+35-LTS-2724
  Encoding: UTF-8 (UTF-8)
  Process: 50922@LOUKASs-Air [192.168.0.207]
  CPUs: 8 - Mem: 16 GB (90.5 MB) - Swap: 2 GB (356.6 MB)
Oct-02 13:51:35.840 [main] DEBUG nextflow.Session - Work-dir: /Users/theodosiou/Documents/Projects/nextflow/nextflow-example/work [Mac OS X]
Oct-02 13:51:35.840 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/theodosiou/Documents/Projects/nextflow/nextflow-example/bin
Oct-02 13:51:35.846 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Oct-02 13:51:35.851 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Oct-02 13:51:35.861 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Oct-02 13:51:35.867 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Oct-02 13:51:35.903 [main] DEBUG nextflow.Session - Session start invoked
Oct-02 13:51:36.227 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Oct-02 13:51:36.235 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: result for class: Script_0f3fefb4
Oct-02 13:51:36.241 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: result for class: Script_0f3fefb4
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:65)
        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:341)
        at Script_0f3fefb4.runScript(Script_0f3fefb4:15)
        at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
        at nextflow.script.BaseScript.run(BaseScript.groovy:217)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:337)
        at nextflow.cli.Launcher.run(Launcher.groovy:480)
        at nextflow.cli.Launcher.main(Launcher.groovy:639)

我查看了其他建议将DSL=1更改为DSL=2的帖子，但这并不影响我的代码。我知道这是个愚蠢的问题，但在这个层次上的一些指导可能会帮助我踢得很顺利。

nextflow

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回答 1

Stack Overflow用户

回答已采纳

发布于 2022-10-02 05:50:27

没有这样的变量:结果

Nextflow抱怨是因为您试图在尚未定义的通道上调用subscribe操作符。使用新的DSL 2，只需定义一个工作流块就可以调用流程：

params.greeting = 'Hello world!'


process test {

    """
    echo '${params.greeting}'
    """
}

workflow {

    test()
}

结果：

$ nextflow run example1.nf 
N E X T F L O W  ~  version 22.04.4
Launching `example1.nf` [suspicious_bell] DSL2 - revision: 71213886a4
executor >  local (1)
[cc/9abb46] process > test [100%] 1 of 1 ✔

然后，要通过通道发送测试过程的stdout，只需定义一个输出块。在这个简单的例子中，您可以在这里使用stdout限定符。要查看输出通道中的项，只需调用视图将其打印到控制台：

params.greeting = 'Hello world!'


process test {

    output:
    stdout

    """
    echo '${params.greeting}'
    """
}

workflow {

    result = test()

    result.view()
}

结果：

$ nextflow run example1.nf 
N E X T F L O W  ~  version 22.04.4
Launching `example1.nf` [curious_raman] DSL2 - revision: 1fa31253d3
executor >  local (1)
[4e/bcd504] process > test [100%] 1 of 1 ✔
Hello world!