Latest edge release wants secrets to be a list #6895
Description
Bug report
The following nf-core module: https://github.com/prototaxites/modules/blob/master/modules/nf-core/mitohifi/findmitoreference/main.nf
Gives the following error when running with Nextflow 26.02.0-edge:
Error executing process > 'SANGERTOL_GENOMEASSEMBLY:GENOMEASSEMBLY:ORGANELLE_ASSEMBLY:MITOHIFI_ASSEMBLY:MITOHIFI_FINDMITOREFERENCE (Caradrina clavipalpis)'
Caused by:
Cannot cast object 'NCBI_API_KEY' with class 'java.lang.String' to class 'java.util.List'
Replacing the secret declaration with:
secret secrets.NCBI_API_KEY ? ["NCBI_API_KEY"] : ""
Fixes the issue in both the current and edge Nextflow release, but this seems incorrect.
Expected behavior and actual behavior
The secret directive should accept a String.
Steps to reproduce the problem
process MITOHIFI_FINDMITOREFERENCE {
tag "$species"
label 'process_single'
secret secrets.NCBI_API_KEY ? "NCBI_API_KEY" : ""
// NOTE: An optional NCBI API key can be supplied to MITOHIFI_FINDMITOREFERENCE.
// This should be set using Nextflow's secrets functionality:
// `nextflow secrets set NCBI_API_KEY <key>`
//
// See https://www.nextflow.io/docs/latest/secrets.html for more information.
// Docker image available at the project github repository
container 'ghcr.io/marcelauliano/mitohifi:3.2.3'
input:
tuple val(meta), val(species)
output:
tuple val(meta), path("*.fasta"), path("*.gb"), emit: reference
// WARN: Incorrect version information is provided by tool on CLI. Please update this string when bumping container versions.
// old version command: \$(mitohifi.py -v | sed 's/.* //')
tuple val("${task.process}"), val('mitohifi'), eval('echo 3.2.3'), emit: versions_mitohifi, topic: versions
when:
task.ext.when == null || task.ext.when
script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "MitoHiFi module does not support Conda. Please use Docker / Singularity instead."
}
def args = task.ext.args ?: ''
def ncbi_api_key = secrets.NCBI_API_KEY ? "--ncbi-api-key \$NCBI_API_KEY" : ""
"""
findMitoReference.py \\
${ncbi_api_key} \\
--species "$species" \\
--outfolder . \\
$args
"""
stub:
"""
touch accession.fasta
touch accession.gb
"""
}
workflow {
MITOHIFI_FINDMITOREFERENCE([[:], "Homo sapiens"])
}
NXF_VER=26.02.0-edge nextflow run main.nf
Program output
Mar-05 14:17:47.365 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf
Mar-05 14:17:47.405 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 26.02.0-edge
Mar-05 14:17:47.422 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/jd42/.nextflow/plugins; core-plugins: nf-amazon@3.7.1,nf-azure@1.22.0,nf-cloudcache@0.6.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.26.1,nf-k8s@1.5.0,nf-seqera@0.12.0,nf-tower@1.21.0,nf-wave@1.18.0
Mar-05 14:17:47.440 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-05 14:17:47.440 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-05 14:17:47.442 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Mar-05 14:17:47.450 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config
Mar-05 14:17:47.520 [main] DEBUG nextflow.plugin.PluginUpdater - Using plugin repository: HttpPluginRepository [registry]; url=https://registry.nextflow.io/api
Mar-05 14:17:47.523 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-05 14:17:47.534 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /Users/jd42/Projects/test/nextflow.config
Mar-05 14:17:47.536 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/jd42/Projects/test/nextflow.config
Mar-05 14:17:47.537 [main] DEBUG nextflow.config.ConfigParserFactory - Using config parser v2
Mar-05 14:17:47.544 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-05 14:17:47.687 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-05 14:17:47.688 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-tower@1.21.0]
Mar-05 14:17:47.814 [main] DEBUG n.plugin.HttpPluginRepository - Registry request: https://registry.nextflow.io/api/v1/plugins/dependencies?plugins=nf-tower%401.21.0&nextflowVersion=26.02.0-edge
- code: 200
- body: {"plugins":[{"id":"nf-tower","releases":[{"version":"1.21.0","url":"https://registry.nextflow.io/api/v1/plugins/nf-tower/1.21.0/download/nf-tower-1.21.0.zip","date":"2026-02-28T12:42:25.708898Z","sha512sum":"3c82b1e34a103b717a38af973eb2a3ddd01b669781be35adf86329936de5f82b140c354e3575274a5d02efc285549ecbdca378a2b0b17946dc2ad89d955b0398","requires":">=26.02.0-edge","dependsOn":[],"status":"PUBLISHED"}],"projectUrl":"https://github.com/nextflow-io/nf-tower","provider":"nextflow-io"}]}
Mar-05 14:17:47.835 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.21.0
Mar-05 14:17:47.841 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.21.0' resolved
Mar-05 14:17:47.841 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.21.0'
Mar-05 14:17:47.855 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.21.0
Mar-05 14:17:47.866 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/jd42/.nextflow/secrets/store.json
Mar-05 14:17:47.867 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@717d7587] - activable => nextflow.secret.LocalSecretsProvider@717d7587
Mar-05 14:17:47.878 [main] DEBUG nextflow.cli.CmdRun - Launching `main.nf` [adoring_joliot] - revision: afb4da46c2
Mar-05 14:17:47.914 [main] DEBUG nextflow.Session - Session UUID: 151e5ef6-a2e0-4c21-9eff-719c02614e0d
Mar-05 14:17:47.914 [main] DEBUG nextflow.Session - Run name: adoring_joliot
Mar-05 14:17:47.915 [main] DEBUG nextflow.Session - Executor pool size: 11
Mar-05 14:17:47.918 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Mar-05 14:17:47.921 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=33; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Mar-05 14:17:47.935 [main] DEBUG nextflow.cli.CmdRun -
Version: 26.02.0-edge build 11371
Created: 28-02-2026 12:06 UTC (12:06 BST)
System: Mac OS X 26.3
Runtime: Groovy 4.0.30 on OpenJDK 64-Bit Server VM 23.0.2+7
Encoding: UTF-8 (UTF-8)
Process: 17554@mib120118s [172.30.35.205]
CPUs: 11 - Mem: 18 GB (70.9 MB) - Swap: 6 GB (1.3 GB)
Mar-05 14:17:47.941 [main] DEBUG nextflow.Session - Work-dir: /Users/jd42/Projects/test/work [Mac OS X]
Mar-05 14:17:47.941 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/jd42/Projects/test/bin
Mar-05 14:17:47.946 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-05 14:17:47.952 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Mar-05 14:17:47.953 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory
Mar-05 14:17:47.960 [main] DEBUG nextflow.Session - Observer factory (v2): TowerFactory
Mar-05 14:17:47.974 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-05 14:17:47.978 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 12; maxThreads: 1000
Mar-05 14:17:48.005 [main] DEBUG nextflow.Session - Session start
Mar-05 14:17:48.008 [main] DEBUG nextflow.script.ScriptLoaderFactory - Using script parser v2
Mar-05 14:17:48.164 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-05 14:17:48.221 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-05 14:17:48.221 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-05 14:17:48.225 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-05 14:17:48.228 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=11; memory=18 GB; capacity=11; pollInterval=100ms; dumpInterval=5m
Mar-05 14:17:48.229 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Mar-05 14:17:48.245 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'MITOHIFI_FINDMITOREFERENCE': maxForks=0; fair=false; array=0
Mar-05 14:17:48.266 [main] DEBUG nextflow.Session - Process names: MITOHIFI_FINDMITOREFERENCE
Mar-05 14:17:48.273 [main] DEBUG nextflow.Session - Igniting dataflow network (2)
Mar-05 14:17:48.274 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > MITOHIFI_FINDMITOREFERENCE
Mar-05 14:17:48.274 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Main: /Users/jd42/Projects/test/main.nf
Mar-05 14:17:48.274 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Mar-05 14:17:48.274 [main] DEBUG nextflow.Session - Session await
Mar-05 14:17:48.332 [Task submitter] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=MITOHIFI_FINDMITOREFERENCE (Homo sapiens); work-dir=/Users/jd42/Projects/test/work/48/9569cc17fcea2157e6bdc69ed613d8
error [org.codehaus.groovy.runtime.typehandling.GroovyCastException]: Cannot cast object 'NCBI_API_KEY' with class 'java.lang.String' to class 'java.util.List'
Mar-05 14:17:48.335 [Task submitter] ERROR nextflow.processor.TaskProcessor - Error executing process > 'MITOHIFI_FINDMITOREFERENCE (Homo sapiens)'
Caused by:
Cannot cast object 'NCBI_API_KEY' with class 'java.lang.String' to class 'java.util.List'
org.codehaus.groovy.runtime.typehandling.GroovyCastException: Cannot cast object 'NCBI_API_KEY' with class 'java.lang.String' to class 'java.util.List'
at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.continueCastOnSAM(DefaultTypeTransformation.java:415)
at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.continueCastOnNumber(DefaultTypeTransformation.java:326)
at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.continueCastOnCollection(DefaultTypeTransformation.java:284)
at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.castToType(DefaultTypeTransformation.java:231)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskConfig.getSecret(TaskConfig.groovy:375)
at nextflow.processor.TaskBean.<init>(TaskBean.groovy:161)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.processor.TaskRun.toTaskBean(TaskRun.groovy:1016)
at nextflow.executor.local.LocalTaskHandler.buildTaskWrapper(LocalTaskHandler.groovy:127)
at nextflow.executor.local.LocalTaskHandler.submit(LocalTaskHandler.groovy:97)
at nextflow.processor.TaskPollingMonitor.submit(TaskPollingMonitor.groovy:275)
at nextflow.processor.LocalPollingMonitor.submit(LocalPollingMonitor.groovy:197)
at nextflow.processor.TaskPollingMonitor.submitPendingTasks(TaskPollingMonitor.groovy:659)
at nextflow.processor.TaskPollingMonitor.submitLoop(TaskPollingMonitor.groovy:470)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1341)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1096)
at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1019)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1215)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1096)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1009)
at groovy.lang.Closure.call(Closure.java:433)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.run(Closure.java:505)
at java.base/java.lang.Thread.run(Thread.java:1575)
Mar-05 14:17:48.337 [Task submitter] DEBUG nextflow.Session - Session aborted -- Cause: Cannot cast object 'NCBI_API_KEY' with class 'java.lang.String' to class 'java.util.List'
Mar-05 14:17:48.344 [Task submitter] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Mar-05 14:17:48.441 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Mar-05 14:17:48.546 [main] DEBUG nextflow.Session - Session await > all processes finished
Mar-05 14:17:48.546 [main] DEBUG nextflow.Session - Session await > all barriers passed
Mar-05 14:17:48.546 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=1; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Mar-05 14:17:48.550 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Mar-05 14:17:48.557 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.21.0'
Mar-05 14:17:48.557 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower
Mar-05 14:17:48.559 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Environment
- Nextflow version: [?]
- Java version: [?]
- Operating system: macOS
- Bash version: (use the command
$SHELL --version)
Additional context
(Add any other context about the problem here)