Change a number of stdout outputs to stderr to not break piped output

See #7116

Signed-off-by: Phil Ewels <phil.ewels@seqera.io>

Author: ewels

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

@@ -469,7 +469,7 @@ class CmdRun extends CmdBase implements HubOptions {
             // Show Nextflow version
             fmt.a(Attribute.INTENSITY_FAINT).a("  ~  ").reset().a("version " + BuildInfo.version).reset()
             fmt.a("\n")
-            AnsiConsole.out.println(fmt.eraseLine())
+            AnsiConsole.err.println(fmt.eraseLine())
         }
         else {
             // Plain header to the console if ANSI is disabled
@@ -527,7 +527,7 @@ class CmdRun extends CmdBase implements HubOptions {
             fmt.fg(Color.CYAN).a("revision: ").reset()
             fmt.fg(Color.CYAN).a(revision).reset()
             fmt.a("\n")
-            AnsiConsole.out().println(fmt.eraseLine())
+            AnsiConsole.err().println(fmt.eraseLine())
         }
         else {
             log.info "${head} [$runName] - revision: ${revision}"

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

@@ -27,7 +27,7 @@ import nextflow.util.LoggerHelper
 
 /**
  * AI agent-friendly log observer that outputs minimal, structured information
- * to standard error, optimized for AI context windows.
+ * to standard output, optimized for AI context windows.
  *
  * Activated via environment variable {@code NXF_AGENT_MODE=1}.
  *

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

@@ -317,7 +317,7 @@ class AnsiLogObserver implements TraceObserverV2, LogObserver {
 
     synchronized protected void renderProgress(WorkflowStats stats) {
         if( printedLines )
-            AnsiConsole.out.println ansi().cursorUp(printedLines+gapLines+1)
+            AnsiConsole.err.println ansi().cursorUp(printedLines+gapLines+1)
 
         // -- print processes
         final term = ansi()
@@ -330,14 +330,14 @@ class AnsiLogObserver implements TraceObserverV2, LogObserver {
 
         final str = term.toString()
         final count = printAndCountLines(str)
-        AnsiConsole.out.flush()
+        AnsiConsole.err.flush()
 
         // usually the gap should be negative because `count` should be greater or equal
         // than the previous `printedLines` value (the output should become longer)
         // otherwise cleanup the remaining lines
         gapLines = printedLines > count ? printedLines-count : 0
         if( gapLines>0 ) for(int i=0; i<gapLines; i++ )
-            AnsiConsole.out.print(ansi().eraseLine().newline())
+            AnsiConsole.err.print(ansi().eraseLine().newline())
         // at the end update the value of printed lines
         printedLines = count
     }
@@ -396,7 +396,7 @@ class AnsiLogObserver implements TraceObserverV2, LogObserver {
                 report += "Failed      : ${stats.failedCountFmt}\n"
 
             printAnsi(report, Color.GREEN, true)
-            AnsiConsole.out.flush()
+            AnsiConsole.err.flush()
         }
     }
 
@@ -407,14 +407,14 @@ class AnsiLogObserver implements TraceObserverV2, LogObserver {
         fmt = fmt.a(message)
         if( bold ) fmt = fmt.boldOff()
         if( color ) fmt = fmt.fg(Color.DEFAULT)
-        AnsiConsole.out.println(fmt.eraseLine())
+        AnsiConsole.err.println(fmt.eraseLine())
     }
 
     protected void printAnsiLines(String lines) {
         final text = lines
                 .replace('\r','')
                 .replace(NEWLINE, ansi().eraseLine().toString() + NEWLINE)
-        AnsiConsole.out.print(text)
+        AnsiConsole.err.print(text)
     }
 
     protected String fmtWidth(String name, int width, int cols) {

modules/nextflow/src/main/groovy/nextflow/util/LoggerHelper.groovy

@@ -718,7 +718,7 @@ class LoggerHelper {
                 final observer = session?.logObserver
                 if( observer ) {
                     if( !observer.started || observer.stopped )
-                        System.out.println(message)
+                        System.err.println(message)
                     else if( event.marker == STICKY )
                         observer.appendSticky(message)
                     else if( event.level==Level.ERROR )
@@ -729,7 +729,7 @@ class LoggerHelper {
                         observer.appendInfo(message)
                 }
                 else {
-                    System.out.println(message)
+                    System.err.println(message)
                 }
             }
             catch (Throwable e) {

modules/nextflow/src/main/groovy/nextflow/util/SpinnerUtil.groovy

@@ -95,8 +95,8 @@ class SpinnerUtil {
                     fmt.a("\r").eraseLine(Erase.ALL)
                     fmt.fg(parseColor(colorName)).a(spinnerChars[spinnerIndex]).reset()
                     fmt.a(" ").a(message)
-                    AnsiConsole.out.print(fmt.toString())
-                    AnsiConsole.out.flush()
+                    AnsiConsole.err.print(fmt.toString())
+                    AnsiConsole.err.flush()
                     spinnerIndex = (spinnerIndex + 1) % spinnerChars.length
                     Thread.sleep(SPINNER_UPDATE_MS)
                 }
@@ -211,8 +211,8 @@ class SpinnerUtil {
         if (ansiEnabled && clearLine) {
             def fmt = Ansi.ansi()
             fmt.a("\r").eraseLine(Erase.ALL)
-            AnsiConsole.out.print(fmt.toString())
-            AnsiConsole.out.flush()
+            AnsiConsole.err.print(fmt.toString())
+            AnsiConsole.err.flush()
         }
 
         spinnerThread = null
@@ -238,10 +238,10 @@ class SpinnerUtil {
             def fmt = Ansi.ansi()
             fmt.a("\r").eraseLine(Erase.ALL)
             fmt.a(finalMessage).a("\n")
-            AnsiConsole.out.print(fmt.toString())
-            AnsiConsole.out.flush()
+            AnsiConsole.err.print(fmt.toString())
+            AnsiConsole.err.flush()
         } else {
-            println finalMessage
+            System.err.println(finalMessage)
         }
 
         spinnerThread = null