[ci fast] Add agent output mode (NXF_AGENT_MODE)

Add AI agent-friendly output mode activated via NXF_AGENT_MODE=1.

When enabled, Nextflow replaces the interactive ANSI progress display with
minimal, structured tagged lines optimized for AI agent context windows:

  [PIPELINE] name version | profile=X
  [WORKDIR] /path/to/work
  [PROCESS hash] name (tag)
  [WARN] deduplicated warning
  [ERROR] name with exit/cmd/stderr/workdir
  [SUCCESS|FAILED] completed=N failed=N cached=N

Key changes:
- LogObserver interface as common abstraction for AnsiLogObserver and AgentLogObserver
- Session holds a single logObserver field instead of two concrete fields
- DefaultObserverFactory creates both observer types using the same pattern
- AgentLogObserver filters hash-prefixed log lines to avoid duplicating [PROCESS] output
- Workflow output (view operator) passes through to stdout in agent mode
- Renamed env var from NXF_AGENT to NXF_AGENT_MODE
- Added NXF_AGENT_MODE to environment variables documentation

Author: edmundmiller

docs/reference/env-vars.md

@@ -16,6 +16,11 @@ The following environment variables control the configuration of the Nextflow ru
 
 ## Nextflow settings
 
+`NXF_AGENT_MODE`
+: :::{versionadded} 26.04.0
+  :::
+: When `true`, enables agent output mode. In this mode, Nextflow replaces the interactive ANSI log with minimal, structured output optimized for AI agents and non-interactive environments. The output uses tagged lines such as `[PIPELINE]`, `[PROCESS]`, `[WARN]`, `[ERROR]`, and `[SUCCESS]`/`[FAILED]` written to standard error (default: `false`).
+
 `NXF_ANSI_LOG`
 : Enables/disables ANSI console output (default `true` when ANSI terminal is detected).
 

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -69,7 +69,7 @@ import nextflow.script.ScriptRunner
 import nextflow.script.WorkflowMetadata
 import nextflow.script.dsl.ProcessConfigBuilder
 import nextflow.spack.SpackConfig
-import nextflow.trace.AnsiLogObserver
+import nextflow.trace.LogObserver
 import nextflow.trace.TraceObserver
 import nextflow.trace.TraceObserverFactory
 import nextflow.trace.TraceObserverFactoryV2
@@ -311,9 +311,11 @@ class Session implements ISession {
 
     boolean ansiLog
 
+    boolean agentLog
+
     boolean disableJobsCancellation
 
-    AnsiLogObserver ansiLogObserver
+    LogObserver logObserver
 
     FilePorter getFilePorter() { filePorter }
 
@@ -832,7 +834,7 @@ class Session implements ISession {
             shutdown0()
             notifyError(null)
             // force termination
-            ansiLogObserver?.forceTermination()
+            logObserver?.forceTermination()
             executorFactory?.signalExecutors()
             processesBarrier.forceTermination()
             monitorsBarrier.forceTermination()
@@ -1278,16 +1280,16 @@ class Session implements ISession {
     }
 
     void printConsole(String str, boolean newLine=false) {
-        if( ansiLogObserver )
-            ansiLogObserver.appendInfo(str)
+        if( logObserver )
+            logObserver.appendInfo(str)
         else if( newLine )
             System.out.println(str)
         else
             System.out.print(str)
     }
 
     void printConsole(Path file) {
-        ansiLogObserver ? ansiLogObserver.appendInfo(file.text) : Files.copy(file, System.out)
+        logObserver ? logObserver.appendInfo(file.text) : Files.copy(file, System.out)
     }
 
     private volatile ThreadPoolManager finalizePoolManager

modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy

@@ -118,6 +118,12 @@ class CliOptions {
         if( noColor ) {
             return ansiLog = false
         }
+
+        // Disable ANSI log in agent mode for plain, parseable output
+        if( SysEnv.isAgentMode() ) {
+            return ansiLog = false
+        }
+
         return Ansi.isEnabled()
     }
 

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -404,7 +404,8 @@ class CmdRun extends CmdBase implements HubOptions {
         runner.setPreview(this.preview, previewAction)
         runner.session.profile = profile
         runner.session.commandLine = launcher.cliString
-        runner.session.ansiLog = launcher.options.ansiLog
+        runner.session.ansiLog = launcher.options.ansiLog && !SysEnv.isAgentMode()
+        runner.session.agentLog = SysEnv.isAgentMode()
         runner.session.debug = launcher.options.remoteDebug
         runner.session.disableJobsCancellation = getDisableJobsCancellation()
 
@@ -435,6 +436,11 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
     protected void printBanner() {
+        // Suppress banner in agent mode for minimal output
+        if( SysEnv.isAgentMode() ) {
+            return
+        }
+
         if( launcher.options.ansiLog ){
             // Plain header for verbose log
             log.debug "N E X T F L O W  ~  version ${BuildInfo.version}"
@@ -499,6 +505,11 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
     protected void printLaunchInfo(String repo, String head, String revision) {
+        // Agent mode output is handled by AgentLogObserver
+        if( SysEnv.isAgentMode() ) {
+            return
+        }
+
         if( launcher.options.ansiLog ){
             log.debug "${head} [$runName] - revision: ${revision}"
 

modules/nextflow/src/main/groovy/nextflow/trace/AgentLogObserver.groovy

@@ -0,0 +1,236 @@
+/*
+ * Copyright 2013-2026, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.trace
+
+import java.util.concurrent.ConcurrentHashMap
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.Session
+import nextflow.processor.TaskRun
+import nextflow.trace.event.TaskEvent
+import nextflow.util.LoggerHelper
+
+/**
+ * AI agent-friendly log observer that outputs minimal, structured information
+ * to standard error, optimized for AI context windows.
+ *
+ * Activated via environment variable {@code NXF_AGENT_MODE=1}.
+ *
+ * Output format:
+ * - {@code [PIPELINE] name version | profile=X}
+ * - {@code [WORKDIR] /path/to/work}
+ * - {@code [PROCESS hash] name (tag)}
+ * - {@code [WARN] warning message} (deduplicated)
+ * - {@code [ERROR] name} with exit/cmd/stderr/workdir
+ * - {@code [SUCCESS|FAILED] completed=N failed=N cached=N}
+ *
+ * @author Edmund Miller <edmund.miller@utdallas.edu>
+ */
+@Slf4j
+@CompileStatic
+class AgentLogObserver implements TraceObserverV2, LogObserver {
+
+    private Session session
+    private WorkflowStatsObserver statsObserver
+    private final Set<String> seenWarnings = ConcurrentHashMap.newKeySet()
+    private volatile boolean started = false
+    private volatile boolean completed = false
+
+    /**
+     * Set the workflow stats observer for retrieving task statistics
+     */
+    void setStatsObserver(WorkflowStatsObserver observer) {
+        this.statsObserver = observer
+    }
+
+    /**
+     * Print a line to standard output (agent format)
+     */
+    protected void println(String line) {
+        System.err.println(line)
+    }
+
+    // -- TraceObserverV2 lifecycle methods --
+
+    @Override
+    void onFlowCreate(Session session) {
+        this.session = session
+    }
+
+    @Override
+    void onFlowBegin() {
+        if( started )
+            return
+        started = true
+
+        // Print pipeline info
+        def manifest = session.manifest
+        def pipelineName = manifest?.name ?: session.scriptName ?: 'unknown'
+        def version = manifest?.version ?: ''
+        def profile = session.profile ?: 'standard'
+
+        def info = "[PIPELINE] ${pipelineName}"
+        if( version )
+            info += " ${version}"
+        info += " | profile=${profile}"
+        println(info)
+
+        // Print work directory
+        def workDir = session.workDir?.toUriString() ?: session.workDir?.toString()
+        if( workDir )
+            println("[WORKDIR] ${workDir}")
+    }
+
+    @Override
+    void onFlowComplete() {
+        if( completed )
+            return
+        completed = true
+        printSummary()
+    }
+
+    @Override
+    void onFlowError(TaskEvent event) {
+        // Error is already reported by onTaskComplete for failed tasks
+    }
+
+    @Override
+    void onTaskSubmit(TaskEvent event) {
+        def task = event.handler?.task
+        if( task )
+            println("[PROCESS ${task.hashLog}] ${task.name}")
+    }
+
+    @Override
+    void onTaskComplete(TaskEvent event) {
+        def handler = event.handler
+        def task = handler?.task
+        if( task?.isFailed() ) {
+            printTaskError(task)
+        }
+    }
+
+    @Override
+    void onTaskCached(TaskEvent event) {
+        // Not reported in agent mode
+    }
+
+    /**
+     * Append a warning message (deduplicated)
+     */
+    void appendWarning(String message) {
+        if( message == null )
+            return
+        // Normalize and deduplicate
+        def normalized = message.trim().replaceAll(/\s+/, ' ')
+        if( seenWarnings.add(normalized) ) {
+            println("[WARN] ${normalized}")
+        }
+    }
+
+    /**
+     * Append an error message
+     */
+    void appendError(String message) {
+        if( message )
+            println("[ERROR] ${message}")
+    }
+
+    /**
+     * Append info message to stdout.
+     * Hash-prefixed task log lines (e.g. {@code [ab/123456] Submitted process > ...})
+     * are filtered out because {@link #onTaskSubmit} already emits a {@code [PROCESS]} line.
+     */
+    void appendInfo(String message) {
+        if( message && !LoggerHelper.isHashLogPrefix(message) )
+            System.out.print(message)
+    }
+
+    /**
+     * Print task error with full diagnostic context
+     */
+    protected void printTaskError(TaskRun task) {
+        def name = task.getName()
+        println("[ERROR] ${name}")
+
+        // Exit status
+        def exitStatus = task.getExitStatus()
+        if( exitStatus != null && exitStatus != Integer.MAX_VALUE ) {
+            println("exit: ${exitStatus}")
+        }
+
+        // Command/script (first line or truncated)
+        def script = task.getScript()?.toString()?.trim()
+        if( script ) {
+            // Truncate long commands
+            def cmd = script.length() > 200 ? script.substring(0, 200) + '...' : script
+            cmd = cmd.replaceAll(/\n/, ' ').replaceAll(/\s+/, ' ')
+            println("cmd: ${cmd}")
+        }
+
+        // Stderr
+        def stderr = task.getStderr()
+        if( stderr ) {
+            def lines = stderr.readLines()
+            if( lines.size() > 10 ) {
+                lines = lines[-10..-1]
+            }
+            println("stderr: ${lines.join(' | ')}")
+        }
+
+        // Stdout (only if relevant)
+        def stdout = task.getStdout()
+        if( stdout && !stderr ) {
+            def lines = stdout.readLines()
+            if( lines.size() > 5 ) {
+                lines = lines[-5..-1]
+            }
+            println("stdout: ${lines.join(' | ')}")
+        }
+
+        // Work directory
+        def workDir = task.getWorkDir()
+        if( workDir ) {
+            println("workdir: ${workDir.toUriString()}")
+        }
+    }
+
+    /**
+     * Print final summary line
+     */
+    protected void printSummary() {
+        def stats = statsObserver?.getStats()
+        def succeeded = stats?.succeededCount ?: 0
+        def failed = stats?.failedCount ?: 0
+        def cached = stats?.cachedCount ?: 0
+        def completed = succeeded + failed
+
+        def status = failed > 0 ? 'FAILED' : 'SUCCESS'
+        println("\n[${status}] completed=${completed} failed=${failed} cached=${cached}")
+    }
+
+    /**
+     * Force termination - called on abort
+     */
+    void forceTermination() {
+        if( !completed ) {
+            completed = true
+            printSummary()
+        }
+    }
+}

modules/nextflow/src/main/groovy/nextflow/trace/AnsiLogObserver.groovy

@@ -39,7 +39,7 @@ import org.fusesource.jansi.AnsiConsole
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
-class AnsiLogObserver implements TraceObserverV2 {
+class AnsiLogObserver implements TraceObserverV2, LogObserver {
 
     static final private String NEWLINE = '\n'
 

modules/nextflow/src/main/groovy/nextflow/trace/DefaultObserverFactory.groovy

@@ -39,6 +39,7 @@ class DefaultObserverFactory implements TraceObserverFactoryV2 {
 
         final result = new ArrayList<TraceObserverV2>(5)
         createAnsiLogObserver(result)
+        createAgentLogObserver(result)
         createGraphObserver(result)
         createReportObserver(result)
         createTimelineObserver(result)
@@ -48,8 +49,18 @@ class DefaultObserverFactory implements TraceObserverFactoryV2 {
 
     protected void createAnsiLogObserver(Collection<TraceObserverV2> result) {
         if( session.ansiLog ) {
-            session.ansiLogObserver = new AnsiLogObserver()
-            result << session.ansiLogObserver
+            def observer = new AnsiLogObserver()
+            session.logObserver = observer
+            result << observer
+        }
+    }
+
+    protected void createAgentLogObserver(Collection<TraceObserverV2> result) {
+        if( session.agentLog ) {
+            def observer = new AgentLogObserver()
+            observer.setStatsObserver(session.statsObserver)
+            session.logObserver = observer
+            result << observer
         }
     }