# Challenging Nextflow workflow - Need help please! **URL:** \ **Category:** Ask for help\ **Tags:** nextflow, nf-core\ **Created:** [January 28, 2025, 10:56pm UTC](https://community.seqera.io/t/challenging-nextflow-workflow-need-help-please/1671 "2025-01-28T22:56:55Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Arkajyoti\_Sarkar](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/arkajyoti_sarkar/32/1399_2.png) [@Arkajyoti\_Sarkar](https://community.seqera.io/u/Arkajyoti_Sarkar)\ **Post date:** [January 28, 2025, 10:56pm UTC](https://community.seqera.io/t/challenging-nextflow-workflow-need-help-please/1671/1 "2025-01-28T22:56:55Z")
Hi everyone, I’m encountering an issue while running my Nextflow workflow written in DSL2. The error suggests there’s an “Unknown process directive: `path`”. Below, I’ve included my workflow script and the error log for reference. ### Nextflow Script: ```groovy #!/usr/bin/env nextflow nextflow.enable.dsl=2 params.input_dir params.output_dir params.diameter_w0 params.diameter_w1 params.flow_threshold_w0 params.flow_threshold_w1 workflow { if (!params.input_dir || !params.output_dir || !params.diameter_w0 || !params.diameter_w1 || !params.flow_threshold_w0 || !params.flow_threshold_w1) { error "All parameters must be provided." } def (w0, w1) = processCellpose( params.input_dir, params.output_dir, params.diameter_w0, params.diameter_w1, params.flow_threshold_w0, params.flow_threshold_w1 ) w0.view { "w0 channel: $it" } w1.view { "w1 channel: $it" } processPlotting( w0, w1, params.input_dir, params.output_dir ) } process processCellpose { container 'cellpose_env:latest' input: val input_dir val output_dir val diameter_w0 val diameter_w1 val flow_threshold_w0 val flow_threshold_w1 output: tuple( path("w0").optional(), path("w1").optional() ) script: """ python /app/cellpose_2ch.py \ --input_dir $input_dir \ --output_dir $PWD \ --diameter_w0 $diameter_w0 \ --diameter_w1 $diameter_w1 \ --flow_threshold_w0 $flow_threshold_w0 \ --flow_threshold_w1 $flow_threshold_w1 mkdir -p ${output_dir}/w0 mkdir -p ${output_dir}/w1 mv w0/* ${output_dir}/w0/ || echo "No files in w0" mv w1/* ${output_dir}/w1/ || echo "No files in w1" """ } process processPlotting { container 'plotting_env:latest' input: path w0 path w1 val input_dir val output_dir output: path("${output_dir}/results") script: """ python /app/nuc_quant.py \ --w0 $w0 \ --w1 $w1 \ --output_rois ${output_dir}/rois \ --output_excel ${output_dir}/excel \ --output_graphs ${output_dir}/graphs \ --intensity_images $input_dir """ } ``` ### Error Log: ```plaintext (base) arka@Dell:~/Desktop/Nextflow_projects/BR_nf$ cat .nextflow.log Jan-28 22:15:39.686 [main] DEBUG nextflow.cli.Launcher - $> nextflow run workflow.nf --input_dir /home/arka/Desktop/Nextflow_projects/BR_nf/input_images --output_dir /home/arka/Desktop/Nextflow_projects/BR_nf/output --diameter_w0 20 --diameter_w1 11.9 --flow_threshold_w0 0.8 --flow_threshold_w1 0.6 Jan-28 22:15:39.835 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.4 Jan-28 22:15:39.862 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/arka/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4 Jan-28 22:15:39.886 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jan-28 22:15:39.888 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jan-28 22:15:39.892 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Jan-28 22:15:39.911 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jan-28 22:15:39.973 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/arka/.nextflow/secrets/store.json Jan-28 22:15:39.988 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1bd81830] - activable => nextflow.secret.LocalSecretsProvider@1bd81830 Jan-28 22:15:40.060 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Jan-28 22:15:40.085 [main] DEBUG nextflow.cli.CmdRun - Launching `workflow.nf` [ridiculous_hoover] DSL2 - revision: 3a841c6dd5 Jan-28 22:15:40.087 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jan-28 22:15:40.088 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jan-28 22:15:40.196 [main] DEBUG nextflow.Session - Session UUID: f0b82bc6-b354-40c8-a8e2-7f50728d7e1e Jan-28 22:15:40.196 [main] DEBUG nextflow.Session - Run name: ridiculous_hoover Jan-28 22:15:40.197 [main] DEBUG nextflow.Session - Executor pool size: 56 Jan-28 22:15:40.208 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Jan-28 22:15:40.216 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=168; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jan-28 22:15:40.254 [main] DEBUG nextflow.cli.CmdRun - Version: 24.10.4 build 5934 Created: 20-01-2025 16:47 UTC (17:47 CEST) System: Linux 6.8.0-51-generic Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 11.0.25+9-post-Ubuntu-1ubuntu122.04 Encoding: UTF-8 (UTF-8) Process: 34911@Dell [127.0.1.1] CPUs: 56 - Mem: 125.8 GB (79.3 GB) - Swap: 2 GB (2 GB) Jan-28 22:15:40.280 [main] DEBUG nextflow.Session - Work-dir: /home/arka/Desktop/Nextflow_projects/BR_nf/work [ext2/ext3] Jan-28 22:15:40.281 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/arka/Desktop/Nextflow_projects/BR_nf/bin Jan-28 22:15:40.294 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jan-28 22:15:40.309 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jan-28 22:15:40.354 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jan-28 22:15:40.369 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 57; maxThreads: 1000 Jan-28 22:15:40.499 [main] DEBUG nextflow.Session - Session start Jan-28 22:15:41.283 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jan-28 22:15:41.438 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_ffb0fc0169112fb4: /home/arka/Desktop/Nextflow_projects/BR_nf/workflow.nf Jan-28 22:15:41.439 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown process directive: `path` Did you mean of these? each Jan-28 22:15:41.445 [main] DEBUG nextflow.Session - Thread[Common-Cleaner,8,InnocuousThreadGroup] java.base@11.0.25/java.lang.Object.wait(Native Method) java.base@11.0.25/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) java.base@11.0.25/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:148) java.base@11.0.25/java.lang.Thread.run(Thread.java:829) java.base@11.0.25/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:161) Thread[Thread-1,5,main] java.base@11.0.25/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.25/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.25/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2123) java.base@11.0.25/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:513) java.base@11.0.25/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:675) app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) java.base@11.0.25/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.25/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.25/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.25/java.lang.reflect.Method.invoke(Method.java:566) app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) app//groovy.lang.Closure.call(Closure.java:433) app//groovy.lang.Closure.call(Closure.java:412) app//groovy.lang.Closure.run(Closure.java:505) java.base@11.0.25/java.lang.Thread.run(Thread.java:829) Thread[AnsiLogObserver,5,main] java.base@11.0.25/java.lang.Object.wait(Native Method) app//nextflow.trace.AnsiLogObserver.render0(AnsiLogObserver.groovy:185) java.base@11.0.25/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) java.base@11.0.25/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) java.base@11.0.25/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.base@11.0.25/java.lang.reflect.Method.invoke(Method.java:566) app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) app//groovy.lang.Closure.call(Closure.java:433) app//groovy.lang.Closure.call(Closure.java:412) app//groovy.lang.Closure.run(Closure.java:505) java.base@11.0.25/java.lang.Thread.run(Thread.java:829) Thread[main,5,main] java.base@11.0.25/java.lang.Thread.dumpThreads(Native Method) java.base@11.0.25/java.lang.Thread.getAllStackTraces(Thread.java:1653) app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) app//nextflow.Session.abort(Session.groovy:800) app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) app//nextflow.cli.Launcher.run(Launcher.groovy:503) app//nextflow.cli.Launcher.main(Launcher.groovy:658) Thread[Finalizer,8,system] java.base@11.0.25/java.lang.Object.wait(Native Method) java.base@11.0.25/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) java.base@11.0.25/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) java.base@11.0.25/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:170) Thread[Signal Dispatcher,9,system] Thread[Reference Handler,10,system] java.base@11.0.25/java.lang.ref.Reference.waitForReferencePendingList(Native Method) java.base@11.0.25/java.lang.ref.Reference.processPendingReferences(Reference.java:241) java.base@11.0.25/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:213) Thread[process reaper,10,system] java.base@11.0.25/jdk.internal.misc.Unsafe.park(Native Method) java.base@11.0.25/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:234) java.base@11.0.25/java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:462) java.base@11.0.25/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:361) java.base@11.0.25/java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:937) java.base@11.0.25/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1053) java.base@11.0.25/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1114) java.base@11.0.25/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) java.base@11.0.25/java.lang.Thread.run(Thread.java:829) Jan-28 22:15:41.455 [main] ERROR nextflow.cli.Launcher - @unknown nextflow.exception.IllegalDirectiveException: Unknown process directive: `path` Did you mean of these? each at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.ProcessConfig.checkName(ProcessConfig.groovy:239) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.ProcessConfig.methodMissing(ProcessConfig.groovy:258) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaClassImpl.invokeMissingMethod(MetaClassImpl.java:924) at groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1413) at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1335) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:391) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:330) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_ffb0fc0169112fb4$_runScript_closure2.doCall(Script_ffb0fc0169112fb4:54) at Script_ffb0fc0169112fb4$_runScript_closure2.doCall(Script_ffb0fc0169112fb4) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.ProcessDef.initialize(ProcessDef.groovy:110) at nextflow.script.ProcessDef.run(ProcessDef.groovy:168) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:103) at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:391) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:330) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_ffb0fc0169112fb4$_runScript_closure1$_closure4.doCall(Script_ffb0fc0169112fb4:20) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) at groovy.lang.Closure.call(Closure.java:433) at groovy.lang.Closure.call(Closure.java:412) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.BaseScript.run0(BaseScript.groovy:198) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.BaseScript.run(BaseScript.groovy:209) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) at nextflow.cli.CmdRun.run(CmdRun.groovy:376) at nextflow.cli.Launcher.run(Launcher.groovy:503) at nextflow.cli.Launcher.main(Launcher.groovy:658) ``` * * * ### Additional Details: 1. **Nextflow Version:** 24.10.4 2. **Command Used to Run:** ```bash nextflow run workflow.nf --input_dir /home/arka/Desktop/Nextflow_projects/BR_nf/input_images --output_dir /home/arka/Desktop/Nextflow_projects/BR_nf/output --diameter_w0 20 --diameter_w1 11.9 --flow_threshold_w0 0.8 --flow_threshold_w1 0.6 ``` 3. **Container Setup:** I’m using `cellpose_env:latest` and `plotting_env:latest` containers. 4. **Expected Behavior:** The script should execute `processCellpose`, produce outputs (`w0` and `w1`), and pass them to `processPlotting`. ### Issue: The workflow fails with the error message: `Unknown process directive: path`. I’ve verified that the `path` directive is valid in DSL2. Could there be an issue with how I’m defining outputs or referencing `path` channels? Any guidance on resolving this issue would be greatly appreciated; I am very new to nextflow and i am still learning. Thanks in advance for your help! Let me know if further details are required. Best regards, Arka ---
**Author:** ![robsyme](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/robsyme/32/342_2.png) [@robsyme](https://community.seqera.io/u/robsyme)\ **Post date:** [January 28, 2025, 11:59pm UTC](https://community.seqera.io/t/challenging-nextflow-workflow-need-help-please/1671/2 "2025-01-28T23:59:35Z")
> [@Arkajyoti\_Sarkar](#): > > ```auto > output: > tuple( > path("w0").optional(), > path("w1").optional() > ) > > ``` I think it’s the way you are specifying optional outputs above. Marking an output as optional is shown as below: ```auto output: tuple path("w0"), path("w1"), optional: true ``` See [docs here](https://www.nextflow.io/docs/latest/process.html#optional-outputs) ---
**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\ **Post date:** [January 29, 2025, 12:04am UTC](https://community.seqera.io/t/challenging-nextflow-workflow-need-help-please/1671/3 "2025-01-29T00:04:23Z")
Hi @Arkajyoti_Sarkar ! Welcome to Seqera Community Forum 🙂 The first issue I see in your code is in the output block of the `processCellpose` process. See the snippet below: ```auto output: tuple( path("w0").optional(), path("w1").optional() ) ``` I wonder from where you got an example like this. This is definitely not the way we write this block. The correct code follows below: ```auto output: tuple path("w0"), path("w1"), optional: true ``` The first thing to realise is that if a you have a tuple as output, the tuple can be optional, or not. You can’t have part of a tuple being optional, so that’s why the `optional` option goes along the line, after the variables. I’d like to take this opportunity to remind you what it means to have an optional output: Normally, if a specified output is not produced by the task, the task will fail. Setting `optional: true` will cause the task to not fail, and instead emit nothing to the given output channel. The second issue is that you seem to be confusing the Nextflow language with something else. Maybe Groovy. The following line doesn’t work as you think: ```auto def (w0, w1) = processCellpose( ``` The `processCellpose` process returns a Nextflow channel and the only way you can handle Nextflow channels is through channel operators. You can’t unpack channels like this just because one or more of its elements is a tuple. You could use a channel operator such as `map` to do something like that, though. The correct way to run this process and `view` what you want is: ```auto .... processCellpose( params.input_dir, params.output_dir, params.diameter_w0, params.diameter_w1, params.flow_threshold_w0, params.flow_threshold_w1 ) processCellpose.out.view { "w0: $it[0]\nw1: $it[1]" } ... ``` I can’t run your code as your instructions to pull these containers do not work, so I changed a bit the code of your process to: ```auto workflow { if (!params.input_dir || !params.output_dir || !params.diameter_w0 || !params.diameter_w1 || !params.flow_threshold_w0 || !params.flow_threshold_w1) { error "All parameters must be provided." } processCellpose( params.input_dir, params.output_dir, params.diameter_w0, params.diameter_w1, params.flow_threshold_w0, params.flow_threshold_w1 ) processCellpose.out.view { "w0: $it[0]\nw1: $it[1]" } } process processCellpose { container 'cellpose_env:latest' input: val input_dir val output_dir val diameter_w0 val diameter_w1 val flow_threshold_w0 val flow_threshold_w1 output: tuple path("w0"), path("w1"), optional: true script: """ touch w0 touch w1 ``` Running like this, you’ll get the following: ![CleanShot 2025-01-28 at 21.06.24@2x](https://europe1.discourse-cdn.com/flex013/uploads/seqera/original/2X/1/137d3d455d09fa04c55a26da417f32fccb757372.jpeg) Oh, one last thing. In your original code, when you view the channel you say something like “w0 channel” and “w1 channel”. This is a misunderstanding ow how it works. The `processCellpose` process has a **single** output channel that consists of elements that individually are tuples. So w0 and w1 are part of a channel element, not channels themselves. I recommend you read the [docs](https://www.nextflow.io/docs/latest/channel.html) and [training materials](https://training.nextflow.io) on Nextflow channels so that this becomes clearer to you, as it’s very important to understand and master other Nextflow concepts.