Semi-regular `ConcurrentModificationException: null` error

[jfy133]

Bug report

We are semi-regularly getting the following ConcurrentModificationException error on nf-core/createtaxdb. See the error and stack trace below.

It happens particularly regularly on GitHub actions, but also sometimes when running locally - particularly when using -resume after an interruption occurs.

The exact process where the error occurs does vary being mostly FIND_CONCATENATE_DNA, sometimes FIND_CONCATENATE_AA (this is the same module imported twice), and very occasionally MALT_BUILD.

Expected behavior and actual behavior

The pipeline runs through without crashing.

Steps to reproduce the problem

Unfortunately this appears to be too complicated to make a minimal reprex, I've tried playing around with various area of the code to see if anything changes but it doesn't appear so.

The fastest way to (maybe) reproduce is:

git clone git@github.com:nf-core/createtaxdb.git && mkdir -p createtaxdb/testing && cd createtaxdb/testing
nextflow run ../main.nf -profile test,docker --outdir ./results --dbname foo

You can try just running a few times to see if it comes up.

But I've found when running locally it's faster to encounter the error by forceably killing the run after a few processes have run, but FIND_CONCATENATE_DNA has not yet started, via ctrl + c.
Then run again but with -resume

nextflow run ../main.nf -profile test,docker --outdir ./results --dbname foo -resume

Program output

Nov-20 13:45:34.898 [Actor Thread 27] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_CREATETAXDB:CREATETAXDB:PREPROCESSING:FIND_CONCATENATE_DNA (1)'

Caused by:
  java.util.ConcurrentModificationException


java.util.ConcurrentModificationException: null
        at java.base/java.util.ArrayList$Itr.checkForComodification(ArrayList.java:1013)
        at java.base/java.util.ArrayList$Itr.next(ArrayList.java:967)
        at nextflow.processor.TaskInputResolver.normalizeInputToFiles(TaskInputResolver.groovy:110)
        at nextflow.processor.TaskInputResolver.resolve(TaskInputResolver.groovy:69)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.selectMethod(IndyInterface.java:355)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.processor.TaskProcessor.resolveTaskInputsV1(TaskProcessor.groovy:1912)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.processor.TaskProcessor.resolveTaskInputs(TaskProcessor.groovy:1851)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.processor.TaskProcessor.invokeTask(TaskProcessor.groovy:670)
        at nextflow.processor.InvokeTaskAdapter.call(InvokeTaskAdapter.groovy:52)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
        at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor.access$001(ForkingDataflowOperatorActor.java:35)
        at groovyx.gpars.dataflow.operator.ForkingDataflowOperatorActor$1.run(ForkingDataflowOperatorActor.java:58)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)
Nov-20 13:45:34.906 [Actor Thread 27] DEBUG nextflow.Session - Session aborted -- Cause: java.util.ConcurrentModificationException

Environment

• Nextflow version: 25.10.0 build 10289
• Java version: openjdk version "17.0.13-internal"
• Operating system: Ubuntu 24.04.3 LTS
• Bash version: GNU bash, version 5.2.21(1)-release (x86_64-pc-linux-gnu)

Additional context

• Originally reported: Intermittent ConcurrentModificationException error #6410
• Initial Slack discussion on nf-core: https://nfcore.slack.com/archives/CE6SDBX2A/p1762520107645479

[pditommaso]

Possibly related (?) #6410

[bentsherman]

This issue is spun out from that one because this co-mod error is coming from a different place