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epi2me-labs / wf-bacterial-genomes

Small variant calling for haploid samples
https://labs.epi2me.io/
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Script compilation error on test dataset #38

Closed jdiazsupsi closed 5 months ago

jdiazsupsi commented 5 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.2.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-bacterial-genomes \ --fastq wf-bacterial-genomes-demo/isolates_fastq \ --isolates \ --sample_sheet wf-bacterial-genomes-demo/isolates_sample_sheet.csv \ -profile standard

Workflow Execution - CLI Execution Profile

None

What happened?

Hello, I tried running the test dataset before using my own data and I get the following error: 

 N E X T F L O W   ~  version 24.04.2

Pulling epi2me-labs/wf-bacterial-genomes ...
 downloaded from https://github.com/epi2me-labs/wf-bacterial-genomes.git
Launching `https://github.com/epi2me-labs/wf-bacterial-genomes` [hopeful_wiles] DSL2 - revision: 6af54574c3 [master]

ERROR ~ Script compilation error
- file : /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/main.nf
- cause: Invalid output definition @ line 862, column 5.
       output(results.all_out)
       ^

1 error

I tried other workflows (like wf-metagenomes) and they work, so it does not seem related to the Nextflow installation. I also tried removing the wf with nextflow drop and downloading it again but the issue persists. Even trying to get the help message by running nextflow run epi2me-labs/wf-bacterial-genomes --help results on the same Script compilation error from above. Do you guys have any idea of what might be causing the issue? Thanks a lot for your time! Best, Juan.

Relevant log output

Jun-26 14:26:54.503 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-bacterial-genomes --fastq wf-bacterial-genomes-demo/isolates_fastq --isolates --sample_sheet wf-bacterial-genomes-demo
/isolates_sample_sheet.csv -profile standard
Jun-26 14:26:54.611 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.04.2
Jun-26 14:26:54.638 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bioinfoserver/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-az
ure@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-26 14:26:54.652 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-26 14:26:54.653 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-26 14:26:54.656 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-26 14:26:54.671 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jun-26 14:26:54.688 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/bioinfoserver/.nextflow/scm
Jun-26 14:26:54.724 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-26 14:26:54.736 [main] INFO  nextflow.cli.CmdRun - Pulling epi2me-labs/wf-bacterial-genomes ...
Jun-26 14:26:54.741 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-bacterial-genomes/contents/nextflow.config
Jun-26 14:26:56.419 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-bacterial-genomes/contents/main.nf
Jun-26 14:26:56.734 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/epi2me-labs/wf-bacterial-genomes
Jun-26 14:26:56.931 [main] DEBUG nextflow.scm.AssetManager - Pulling epi2me-labs/wf-bacterial-genomes -- Using remote clone url: https://github.com/epi2me-labs/wf-bacterial-genomes.git
Jun-26 14:27:06.109 [main] INFO  nextflow.cli.CmdRun -  downloaded from https://github.com/epi2me-labs/wf-bacterial-genomes.git
Jun-26 14:27:06.143 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config
Jun-26 14:27:06.145 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/nextflow.config
Jun-26 14:27:06.152 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bioinfoserver/.nextflow/secrets/store.json
Jun-26 14:27:06.156 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@578a5ce8] - activable => nextflow.secret.LocalSecretsProvider@578a5ce8
Jun-26 14:27:06.168 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-26 14:27:06.404 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-26 14:27:06.405 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-bacterial-genomes` [hopeful_wiles] DSL2 - revision: 6af54574c3 [master]
Jun-26 14:27:06.407 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-26 14:27:06.407 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-26 14:27:06.477 [main] DEBUG nextflow.Session - Session UUID: cb1ae23f-847d-4221-90d7-8f22e4fd2928
Jun-26 14:27:06.477 [main] DEBUG nextflow.Session - Run name: hopeful_wiles
Jun-26 14:27:06.478 [main] DEBUG nextflow.Session - Executor pool size: 28
Jun-26 14:27:06.490 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-26 14:27:06.518 [main] DEBUG nextflow.cli.CmdRun -
  Version: 24.04.2 build 5914
  Created: 29-05-2024 06:19 UTC (08:19 CEST)
  System: Linux 4.15.0-213-generic
  Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 21-internal-adhoc.conda.src
  Encoding: UTF-8 (UTF-8)
  Process: 28691@bioinfoserver [127.0.1.1]
  CPUs: 28 - Mem: 251.4 GB (192.9 GB) - Swap: 976 MB (975 MB) - Virtual threads ON
Jun-26 14:27:06.552 [main] DEBUG nextflow.Session - Work-dir: /home/bioinfoserver/projects/juan/bet/miboc/epi2me/work [ext2/ext3]
Jun-26 14:27:06.588 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-26 14:27:06.603 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-26 14:27:06.682 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-26 14:27:06.691 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
Jun-26 14:27:06.761 [main] DEBUG nextflow.Session - Session start
Jun-26 14:27:06.765 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/bioinfoserver/projects/juan/bet/miboc/epi2me/output/execution/trace.txt
Jun-26 14:27:06.770 [main] DEBUG nextflow.Session - Using default localLib path: /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib
Jun-26 14:27:06.774 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib
Jun-26 14:27:06.774 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/lib/nfcore_external_java_deps.jar
Jun-26 14:27:07.996 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Jun-26 14:27:08.004 [main] ERROR nextflow.cli.Launcher - Script compilation error
- file : /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/main.nf
- cause: Invalid output definition @ line 862, column 5.
       output(results.all_out)
       ^

1 error

nextflow.exception.ScriptCompilationException: Script compilation error
- file : /home/bioinfoserver/.nextflow/assets/epi2me-labs/wf-bacterial-genomes/main.nf
- cause: Invalid output definition @ line 862, column 5.
       output(results.all_out)
       ^

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_e5c63c8040c5e648: 862: Invalid output definition @ line 862, column 5.
       output(results.all_out)
       ^

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 5 months ago

Hi @jdiazsupsi, Nextflow introduced a new feature in v24.04 that conflicts with some of our workflows. This will be fixed in the next wf-bacterial-genomes release. In the meantime, you can run the workflow with Nextflow version 23.10 by running it as

NXF_VER=23.10.1 nextflow run epi2me-labs/wf-bacterial-genomes ...

Please let us know if this doesn't resolve the issue. Thanks for your patience!

jdiazsupsi commented 5 months ago

Hi @julibeg, I created a new conda environment with Nextflow 23.10.1 and it run to completion. Thanks a lot for the quick solution!