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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Invalid output definition when I try to run test data #111

Closed MauriAndresMU1313 closed 2 months ago

MauriAndresMU1313 commented 2 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v3.10.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-artic --fastq ./wf-artic-demo/fastq/ -profile standard

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I'm trying to run the test data after downloading the test dataset provided by https://github.com/epi2me-labs/wf-artic I have Docker installed (version 26.1.4) and my Java version:

openjdk version "11.0.23" 2024-04-16
OpenJDK Runtime Environment (build 11.0.23+9-post-Ubuntu-1ubuntu122.04.1)
OpenJDK 64-Bit Server VM (build 11.0.23+9-post-Ubuntu-1ubuntu122.04.1, mixed mode, sharing)

My wf-artic-demo directory looks like this:

fastq  md5sums.txt  nextflow.config  output  README  sample_sheet.csv  work

So far, when I tried to run this test line:

nextflow run epi2me-labs/wf-artic --fastq ./wf-artic-demo/fastq/ -profile standard

I got the following error:

Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
Script_e4f9eb14011d9e79: 638: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error

    at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:292)
    at org.codehaus.groovy.control.CompilationUnit$IPrimaryClassNodeOperation.doPhaseOperation(CompilationUnit.java:980)
    at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:692)
    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:666)
    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:373)
    at groovy.lang.GroovyClassLoader.lambda$parseClass$2(GroovyClassLoader.java:316)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
    at groovy.lang.GroovyShell.parseClass(GroovyShell.java:572)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:585)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:639)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:643)
    at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:175)
    ... 6 common frames omitted

I could not figure out what is the issue.

Relevant log output

Jun-17 19:51:27.779 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-artic --fastq ./wf-artic-demo/fastq/ -profile standard
Jun-17 19:51:27.878 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-17 19:51:27.912 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/mmora30/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jun-17 19:51:27.932 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-17 19:51:27.934 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-17 19:51:27.939 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-17 19:51:27.965 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-17 19:51:27.990 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/mmora30/.nextflow/scm
Jun-17 19:51:28.992 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-artic.git
Jun-17 19:51:29.035 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-17 19:51:29.048 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/.git/config; branch: master; remote: origin; url: https://github.com/epi2me-labs/wf-artic.git
Jun-17 19:51:29.772 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Jun-17 19:51:29.773 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/mmora30/workspace/nextflow_pipelines/wf-artic-demo/nextflow.config
Jun-17 19:51:29.775 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/nextflow.config
Jun-17 19:51:29.776 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mmora30/workspace/nextflow_pipelines/wf-artic-demo/nextflow.config
Jun-17 19:51:29.785 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/mmora30/.nextflow/secrets/store.json
Jun-17 19:51:29.789 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@392781e] - activable => nextflow.secret.LocalSecretsProvider@392781e
Jun-17 19:51:29.803 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-17 19:51:30.020 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-17 19:51:30.081 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-17 19:51:30.083 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-artic` [cranky_meninsky] DSL2 - revision: cf4041c563 [master]
Jun-17 19:51:30.085 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-17 19:51:30.085 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-17 19:51:30.166 [main] DEBUG nextflow.Session - Session UUID: 6970c700-3c0d-496c-95c6-97e001be947d
Jun-17 19:51:30.167 [main] DEBUG nextflow.Session - Run name: cranky_meninsky
Jun-17 19:51:30.168 [main] DEBUG nextflow.Session - Executor pool size: 24
Jun-17 19:51:30.180 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-17 19:51:30.187 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-17 19:51:30.213 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC
  System: Linux 5.15.0-112-generic
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.23+9-post-Ubuntu-1ubuntu122.04.1
  Encoding: UTF-8 (UTF-8)
  Process: 123242@medina-lab [127.0.1.1]
  CPUs: 24 - Mem: 122.8 GB (95 GB) - Swap: 8 GB (8 GB)
Jun-17 19:51:30.243 [main] DEBUG nextflow.Session - Work-dir: /home/mmora30/workspace/nextflow_pipelines/wf-artic-demo/work [ext2/ext3]
Jun-17 19:51:30.307 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-17 19:51:30.332 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-17 19:51:30.444 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-17 19:51:30.461 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jun-17 19:51:30.548 [main] DEBUG nextflow.Session - Session start
Jun-17 19:51:30.551 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/mmora30/workspace/nextflow_pipelines/wf-artic-demo/output/execution/trace.txt
Jun-17 19:51:30.560 [main] DEBUG nextflow.Session - Using default localLib path: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/lib
Jun-17 19:51:30.566 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/lib
Jun-17 19:51:30.566 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/lib/nfcore_external_java_deps.jar
Jun-17 19:51:31.985 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Jun-17 19:51:31.994 [main] ERROR nextflow.cli.Launcher - Script compilation error
- file : /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/main.nf
- cause: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error

nextflow.exception.ScriptCompilationException: Script compilation error
- file : /home/mmora30/.nextflow/assets/epi2me-labs/wf-artic/main.nf
- cause: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error

    at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:196)
    at nextflow.script.ScriptParser.parse(ScriptParser.groovy:206)
    at nextflow.script.ScriptRunner.parseScript(ScriptRunner.groovy:229)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:136)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
    at nextflow.cli.Launcher.run(Launcher.groovy:503)
    at nextflow.cli.Launcher.main(Launcher.groovy:657)
Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
Script_e4f9eb14011d9e79: 638: Invalid output definition @ line 638, column 5.
       output(results)
       ^

1 error

    at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:292)
    at org.codehaus.groovy.control.CompilationUnit$IPrimaryClassNodeOperation.doPhaseOperation(CompilationUnit.java:980)
    at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:692)
    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:666)
    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:373)
    at groovy.lang.GroovyClassLoader.lambda$parseClass$2(GroovyClassLoader.java:316)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
    at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
    at groovy.lang.GroovyShell.parseClass(GroovyShell.java:572)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:585)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:639)
    at groovy.lang.GroovyShell.parse(GroovyShell.java:643)
    at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:175)
    ... 6 common frames omitted

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response

julibeg commented 2 months ago

Hi @MauriAndresMU1313, this issue is due to an incompatibility of a new feature introduced in the latest Nextflow version with some of our workflows. It will be fixed in the next wf-artic release. In the meantime, you can run the workflow with an older version of Nextflow as follows

NXF_VER=23.10.1 nextflow run epi2me-labs/wf-artic --fastq ./wf-artic-demo/fastq/ -profile standard

Many thanks for your patience!

MauriAndresMU1313 commented 2 months ago

Thank you for your quick response! I will check with that option