Nextflow 教程出现错误 "no such variable"

Question

我正在尝试学习 nextflow，但不是很顺利。我从这个站点的教程开始：https://www.nextflow.io/docs/latest/getstarted.html（我是安装 nextflow 的人）。

我复制了这个脚本：

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process splitLetters {

    output:
    file 'chunk_*' into letters

    """
    printf '${params.str}' | split -b 6 - chunk_
    """
}


process convertToUpper {

    input:
    file x from letters.flatten()

    output:
    stdout result

    """
    cat $x | tr '[a-z]' '[A-Z]'
    """
}

result.view { it.trim() }

但是当我运行它时（nextflow 运行 tutorial.nf），在终端我有这个：

N E X T F L O W  ~  version 22.03.1-edge
Launching `tutorial.nf` [intergalactic_waddington] DSL2 - revision: be42f295f4
No such variable: result

 -- Check script 'tutorial.nf' at line: 29 or see '.nextflow.log' file for more details

在日志文件中我有这个：

avr.-20 14:14:12.319 [main] DEBUG nextflow.cli.Launcher - $> nextflow run tutorial.nf
avr.-20 14:14:12.375 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 22.03.1-edge
avr.-20 14:14:12.466 [main] INFO  nextflow.cli.CmdRun - Launching `tutorial.nf` [intergalactic_waddington] DSL2 - revision: be42f295f4
avr.-20 14:14:12.481 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/user/.nextflow/plugins; core-plugins: nf-amazon@1.6.0,nf-azure@0.13.0,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.3.0,nf-tower@1.4.0
avr.-20 14:14:12.483 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
avr.-20 14:14:12.494 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
avr.-20 14:14:12.495 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
avr.-20 14:14:12.501 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
avr.-20 14:14:12.515 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
avr.-20 14:14:12.571 [main] DEBUG nextflow.Session - Session uuid: 67344021-bff5-4131-9c07-e101756fb5ea
avr.-20 14:14:12.571 [main] DEBUG nextflow.Session - Run name: intergalactic_waddington
avr.-20 14:14:12.573 [main] DEBUG nextflow.Session - Executor pool size: 8
avr.-20 14:14:12.604 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 22.03.1-edge build 5695
avr.-20 14:14:12.629 [main] DEBUG nextflow.Session - Work-dir: /home/user/Documents/formations/nextflow/testScript/work [ext2/ext3]
avr.-20 14:14:12.629 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/user/Documents/formations/nextflow/testScript/bin
avr.-20 14:14:12.637 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
avr.-20 14:14:12.648 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
avr.-20 14:14:12.669 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
avr.-20 14:14:12.678 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
avr.-20 14:14:12.741 [main] DEBUG nextflow.Session - Session start invoked
avr.-20 14:14:13.423 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
avr.-20 14:14:13.446 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: result for class: Script_6634cd79
avr.-20 14:14:13.463 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: result for class: Script_6634cd79
        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_6634cd79.runScript(Script_6634cd79:29)
        at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
        at nextflow.script.BaseScript.run(BaseScript.groovy:203)
        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:334)
        at nextflow.cli.Launcher.run(Launcher.groovy:480)
        at nextflow.cli.Launcher.main(Launcher.groovy:639)

我该怎么办？非常感谢您的帮助。

Answer 1

Nextflow 包含一个名为 DSL2 的新语言扩展，它成为 version 22.03.0-edge 中的 default 语法.但是，可以通过在脚本顶部添加 nextflow.enable.dsl=1 或在运行脚本时设置 -dsl1 选项来覆盖此行为：

nextflow run tutorial.nf -dsl1

或者，回滚到最新版本（而不是 'edge' pre-release）。可以使用 NXF_VER 环境变量指定 Nextflow 版本：

NXF_VER=21.10.6 nextflow run tutorial.nf

我发现 DSL2 极大地简化了复杂工作流程的编写，强烈建议您开始使用它。不幸的是，文档有点滞后，但是一旦你掌握了窍门，将它翻过来就相对简单了：

params.str = 'Hello world!'


process splitLetters {

    output:
    path 'chunk_*'

    """
    printf '${params.str}' | split -b 6 - chunk_
    """
}


process convertToUpper {

    input:
    path x

    output:
    stdout

    """
    cat $x | tr '[a-z]' '[A-Z]'
    """
}


workflow {

    splitLetters | flatten() | convertToUpper | view()
}

结果：

nextflow run tutorial.nf -dsl2
N E X T F L O W  ~  version 21.10.6
Launching `tutorial.nf` [prickly_kilby] - revision: 0c6f835b9c
executor >  local (3)
[b8/84a1de] process > splitLetters       [100%] 1 of 1 ✔
[86/fd19ea] process > convertToUpper (2) [100%] 2 of 2 ✔
HELLO 
WORLD!

Nextflow 教程出现错误 "no such variable"

Nextflow tutorial getting error "no such variable"

nextflow