When files from different processess have the same name, workflow outputs only copy one file

Bug report

Expected behavior and actual behavior

I have two processes that both create files with the same name.
I expect to be able to publish both files and update the names in the output block.

Instead, only the second file gets output. eg:

output {
    profiles {
        mode 'copy'
        path { out ->
            // A file named "pyspy.prof" from the PROFILE_A process
            out.profile_a >> "pyspy/${out.meta.id}.profile_a.pyspy.prof"
            // A file named "pyspy.prof" from the PROFILE_B process
            out.profile_b >> "pyspy/${out.meta.id}.profile_b.pyspy.prof"
}}}

I would expect to get outputs such as:

results
└── pyspy
    ├── case001.profile_a.pyspy.prof
    ├── case001.profile_b.pyspy.prof
    ├── case002.profile_a.pyspy.prof
    └── case002.profile_b.pyspy.prof

But what I actually get is:

results
└── pyspy
    ├── case001.profile_b.pyspy.prof
    └── case002.profile_b.pyspy.prof

Furthermore, the file content is incorrect:

head ./results/pyspy/*

==> ./results/pyspy/case001.profile_b.pyspy.prof <==
PROFILE_A

==> ./results/pyspy/case002.profile_b.pyspy.prof <==
PROFILE_B

I can confirm that the files were not mis-attributed in the join. The following is the output from the toy example below:

[meta:[id:case001], profile_a:/Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/87/0de5c7ec9482e8f25a0f8d0e553bc6/pyspy.prof, profile_b:/Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/89/ad6c7974848a11b1fba224b09f0023/pyspy.prof]
[meta:[id:case002], profile_a:/Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/56/5827cde5334bde58db0053e8300bc8/pyspy.prof, profile_b:/Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/df/012645b58f7fe7a0b7ca189b6f02ed/pyspy.prof]

And the file content:

cat /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/87/0de5c7ec9482e8f25a0f8d0e553bc6/pyspy.prof
PROFILE_A
cat /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/89/ad6c7974848a11b1fba224b09f0023/pyspy.prof
PROFILE_B
cat /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/56/5827cde5334bde58db0053e8300bc8/pyspy.prof
PROFILE_A
cat /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/df/012645b58f7fe7a0b7ca189b6f02ed/pyspy.prof
PROFILE_B

Steps to reproduce the problem

The following example can reproduce the issue:

workflow {
    main:
    ch_cases = channel.of('case001','case002')
    PROFILE_A(ch_cases)
    PROFILE_B(ch_cases)

    ch_profiles = PROFILE_A.out.profiles.join(PROFILE_B.out.profiles)
        .map { caseid, profile_a, profile_b ->
            [
                meta:[ id: caseid ],
                profile_a: profile_a,
                profile_b: profile_b
            ]
        }
    ch_profiles.view()


    publish:
    profiles = ch_profiles
}

output {
    profiles {
        mode 'copy'
        path { out ->
            out.profile_a >> "pyspy/${out.meta.id}.profile_a.pyspy.prof"
            out.profile_b >> "pyspy/${out.meta.id}.profile_b.pyspy.prof"
        }
    }
}

process PROFILE_A {
    input:
    val caseid

    script:
    """
    echo "PROFILE_A" > pyspy.prof
    """

    output:
    tuple val(caseid), path("pyspy.prof"), emit: profiles
}

process PROFILE_B {
    input:
    val caseid

    script:
    """
    echo "PROFILE_B" > pyspy.prof
    """

    output:
    tuple val(caseid), path("pyspy.prof"), emit: profiles
}

Program output

Nov-27 15:44:12.308 [main] DEBUG nextflow.cli.Launcher - $> nextflow run ./main.nf
Nov-27 15:44:12.356 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 25.10.0
Nov-27 15:44:12.410 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/gabrielaldam/.nextflow/plugins; core-plugins: nf-amazon@3.4.1,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.3,nf-k8s@1.2.2,nf-tower@1.17.1,nf-wave@1.16.1
Nov-27 15:44:12.425 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Nov-27 15:44:12.426 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Nov-27 15:44:12.427 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Nov-27 15:44:12.436 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config
Nov-27 15:44:12.534 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Nov-27 15:44:12.535 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Nov-27 15:44:12.535 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Nov-27 15:44:12.545 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/gabrielaldam/.nextflow/secrets/store.json
Nov-27 15:44:12.550 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@67c277a0] - activable => nextflow.secret.LocalSecretsProvider@67c277a0
Nov-27 15:44:12.572 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Nov-27 15:44:12.588 [main] DEBUG nextflow.cli.CmdRun - Launching `./main.nf` [festering_mahavira] DSL2 - revision: d5c3127ffd
Nov-27 15:44:12.619 [main] DEBUG nextflow.Session - Session UUID: d0d03db4-48d4-48a0-8f82-5cc3c25072ee
Nov-27 15:44:12.619 [main] DEBUG nextflow.Session - Run name: festering_mahavira
Nov-27 15:44:12.619 [main] DEBUG nextflow.Session - Executor pool size: 8
Nov-27 15:44:12.624 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Nov-27 15:44:12.627 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Nov-27 15:44:12.648 [main] DEBUG nextflow.cli.CmdRun -
  Version: 25.10.0 build 10289
  Created: 22-10-2025 16:26 UTC (17:26 BST)
  System: Mac OS X 26.1
  Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.15+6-LTS
  Encoding: UTF-8 (UTF-8)
  Process: 81021@GEL-G9C747KD9H [10.255.51.115]
  CPUs: 8 - Mem: 16 GB (76 MB) - Swap: 6 GB (1.1 GB)
Nov-27 15:44:12.657 [main] DEBUG nextflow.Session - Work-dir: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work [Mac OS X]
Nov-27 15:44:12.657 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/bin
Nov-27 15:44:12.662 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Nov-27 15:44:12.666 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Nov-27 15:44:12.667 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory
Nov-27 15:44:12.686 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Nov-27 15:44:12.691 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Nov-27 15:44:12.721 [main] DEBUG nextflow.Session - Session start
Nov-27 15:44:13.042 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Nov-27 15:44:13.104 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 15:44:13.105 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 15:44:13.109 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Nov-27 15:44:13.112 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=16 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
Nov-27 15:44:13.113 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Nov-27 15:44:13.128 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROFILE_A': maxForks=0; fair=false; array=0
Nov-27 15:44:13.148 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Nov-27 15:44:13.148 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Nov-27 15:44:13.149 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROFILE_B': maxForks=0; fair=false; array=0
Nov-27 15:44:13.169 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: PROFILE_A, PROFILE_B
Nov-27 15:44:13.170 [main] DEBUG nextflow.Session - Igniting dataflow network (3)
Nov-27 15:44:13.170 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PROFILE_A
Nov-27 15:44:13.170 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > PROFILE_B
Nov-27 15:44:13.171 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_50d6b2ddf702c0dd: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/main.nf
Nov-27 15:44:13.171 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Nov-27 15:44:13.171 [main] DEBUG nextflow.Session - Session await
Nov-27 15:44:13.246 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-27 15:44:13.247 [Task submitter] INFO  nextflow.Session - [87/0de5c7] Submitted process > PROFILE_A (1)
Nov-27 15:44:13.252 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-27 15:44:13.252 [Task submitter] INFO  nextflow.Session - [df/012645] Submitted process > PROFILE_B (2)
Nov-27 15:44:13.256 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-27 15:44:13.256 [Task submitter] INFO  nextflow.Session - [89/ad6c79] Submitted process > PROFILE_B (1)
Nov-27 15:44:13.260 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Nov-27 15:44:13.260 [Task submitter] INFO  nextflow.Session - [56/5827cd] Submitted process > PROFILE_A (2)
Nov-27 15:44:13.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: PROFILE_A (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/87/0de5c7ec9482e8f25a0f8d0e553bc6]
Nov-27 15:44:13.324 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Nov-27 15:44:13.325 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: PROFILE_B (2); status: COMPLETED; exit: 0; error: -; workDir: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/df/012645b58f7fe7a0b7ca189b6f02ed]
Nov-27 15:44:13.326 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: PROFILE_B (1); status: COMPLETED; exit: 0; error: -; workDir: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/89/ad6c7974848a11b1fba224b09f0023]
Nov-27 15:44:13.326 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: PROFILE_A (2); status: COMPLETED; exit: 0; error: -; workDir: /Users/gabrielaldam/Projects/consolidate_abtiering/fail/work/56/5827cde5334bde58db0053e8300bc8]
Nov-27 15:44:13.360 [main] DEBUG nextflow.Session - Session await > all processes finished
Nov-27 15:44:13.373 [Actor Thread 6] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Nov-27 15:44:13.419 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Nov-27 15:44:13.419 [main] DEBUG nextflow.Session - Session await > all barriers passed
Nov-27 15:44:13.421 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false)
Nov-27 15:44:13.421 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Nov-27 15:44:13.424 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=4; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=4; peakMemory=0; ]
Nov-27 15:44:13.627 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Nov-27 15:44:13.635 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Nov-27 15:44:13.635 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Environment

• Nextflow version: nextflow version 25.10.0.10289
• Java version: OpenJDK 64-Bit Server VM Homebrew (build 22, mixed mode, sharing)
• Operating system: macOS (26.1 (25B78))
• Bash version: zsh 5.9 (arm64-apple-darwin25.0)

Additional context

(Add any other context about the problem here)

Start by running the supplied main.nf reproduction and inspect the output block's publish path handling for the joined profile_a and profile_b files. Trace how duplicate source filenames are tracked during publishing. Done means both files from each case are copied to their distinct renamed paths with their original contents preserved.