Fix nextflow lint ignoring --quiet flag

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

@@ -82,6 +82,9 @@ class CmdLint extends CmdBase {
         }
     }
 
+    @Parameter(names = ['-q', '-quiet'], description = 'Suppress progress messages (file-by-file status and summary); errors are still shown')
+    boolean quiet
+
     @Parameter(names = ['-format'], description = 'Format scripts and config files that have no errors')
     boolean formatting
 
@@ -127,7 +130,7 @@ class CmdLint extends CmdBase {
             ? new JsonErrorListener()
             : outputMode == 'markdown'
             ? new MarkdownErrorListener()
-            : new StandardErrorListener(outputMode, launcher.options.ansiLog)
+            : new StandardErrorListener(outputMode, launcher.options.ansiLog, quiet || launcher.options.quiet)
         formattingOptions = new FormattingOptions(spaces, !tabs, harhsilAlignment, false, sortDeclarations)
 
         errorListener.beforeAll()

modules/nextflow/src/main/groovy/nextflow/script/parser/v2/ErrorListener.groovy

@@ -55,40 +55,66 @@ class ErrorSummary {
 class StandardErrorListener implements ErrorListener {
     private String mode
     private boolean ansiLog
+    /** When true, suppress progress/summary messages (file-by-file status and
+     *  the final summary).  Errors and warnings are always shown.
+     *  Automatically set when ansiLog is false (non-interactive output) or
+     *  when the global --quiet / -q flag is active. */
+    private boolean suppressProgress
 
-    StandardErrorListener(String mode, boolean ansiLog) {
+    StandardErrorListener(String mode, boolean ansiLog, boolean quiet=false) {
         this.mode = mode
         this.ansiLog = ansiLog
+        // Suppress the animated progress lines whenever ANSI is off (they
+        // rely on cursor-up/erase-line sequences) or when the caller has
+        // explicitly requested quiet mode.
+        this.suppressProgress = !ansiLog || quiet
     }
 
     private Ansi ansi() {
-        final ansi = Ansi.ansi()
-        ansi.setEnabled(ansiLog)
-        return ansi
+        // Ansi.setEnabled() is static-only in Jansi 2.x: codes are baked into
+        // the Ansi buffer when fg()/bold() etc. are called, not at toString()
+        // time.  Set the global flag here so every Ansi object created by this
+        // listener appends codes only when ansiLog=true.
+        Ansi.setEnabled(ansiLog)
+        return Ansi.ansi()
+    }
+
+    private void print(Object text) {
+        final str = text.toString()
+        if( ansiLog ) {
+            // AnsiConsole.out handles TTY detection: renders ANSI on a terminal,
+            // strips codes when output is piped.
+            AnsiConsole.out.print(str)
+            AnsiConsole.out.flush()
+        }
+        else {
+            System.out.print(str)
+            System.out.flush()
+        }
     }
 
     @Override
     void beforeAll() {
-        final line = ansi().a("Linting Nextflow code..").newline()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
+        if( suppressProgress )
+            return
+        print(ansi().a("Linting Nextflow code..").newline())
     }
 
     @Override
     void beforeFile(File file) {
-        final line = ansi()
+        if( suppressProgress )
+            return
+        print(ansi()
             .cursorUp(1).eraseLine()
             .a(Ansi.Attribute.INTENSITY_FAINT).a("Linting: ${file}")
-            .reset().newline().toString()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
+            .reset().newline())
     }
 
     private Ansi term
 
     @Override
     void beforeErrors() {
-        term = ansi().cursorUp(1).eraseLine()
+        term = suppressProgress ? ansi() : ansi().cursorUp(1).eraseLine()
     }
 
     @Override
@@ -215,26 +241,28 @@ class StandardErrorListener implements ErrorListener {
 
     @Override
     void afterErrors() {
-        // print extra newline since next file status will chomp back one
-        term.fg(Ansi.Color.DEFAULT).newline()
-        AnsiConsole.out.print(term)
-        AnsiConsole.out.flush()
+        if( !suppressProgress ) {
+            // print extra newline since next file status will chomp back one
+            term.fg(Ansi.Color.DEFAULT).newline()
+        }
+        print(term)
     }
 
     @Override
     void beforeFormat(File file) {
-        final line = ansi()
+        if( suppressProgress )
+            return
+        print(ansi()
             .cursorUp(1).eraseLine()
             .a(Ansi.Attribute.INTENSITY_FAINT).a("Formatting: ${file}")
-            .reset().newline().toString()
-        AnsiConsole.out.print(line)
-        AnsiConsole.out.flush()
+            .reset().newline())
     }
 
     @Override
     void afterAll(ErrorSummary summary) {
         final term = ansi()
-        term.cursorUp(1).eraseLine()
+        if( !suppressProgress )
+            term.cursorUp(1).eraseLine()
         // print extra newline if no code is being shown
         if( mode == 'concise' )
             term.newline()
@@ -254,8 +282,7 @@ class StandardErrorListener implements ErrorListener {
         if( summary.filesWithErrors == 0 && summary.filesWithoutErrors == 0 ) {
             term.a(" No files found to process").newline()
         }
-        AnsiConsole.out.print(term)
-        AnsiConsole.out.flush()
+        print(term)
     }
 
     private static record Range(

modules/nextflow/src/test/groovy/nextflow/cli/CmdLintTest.groovy

@@ -81,4 +81,151 @@ class CmdLintTest extends Specification {
         dir?.deleteDir()
     }
 
+    def 'should suppress progress with nextflow -q lint (global quiet flag)'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+                script:
+                "echo hello"
+            }
+            '''
+
+        when:
+        def cmd = new CmdLint()
+        cmd.args = [dir.toFile().toString()]
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions) {
+                isQuiet() >> true
+                getAnsiLog() >> false
+            }
+        }
+        cmd.run()
+
+        then:
+        noExceptionThrown()
+        and:
+        !capture.toString().contains("Linting Nextflow code")
+        !capture.toString().contains("Linting:")
+        and:
+        capture.toString().contains("Nextflow linting complete")
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+    def 'should suppress progress when ansiLog is false (non-interactive output)'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+                script:
+                "echo hello"
+            }
+            '''
+
+        when:
+        def cmd = new CmdLint()
+        cmd.args = [dir.toFile().toString()]
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions) {
+                isQuiet() >> false
+                getAnsiLog() >> false
+            }
+        }
+        cmd.run()
+
+        then:
+        noExceptionThrown()
+        and:
+        !capture.toString().contains("Linting Nextflow code")
+        !capture.toString().contains("Linting:")
+        and:
+        capture.toString().contains("Nextflow linting complete")
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+    def 'should suppress progress with lint -q flag (lint-level quiet, keeps ANSI)'() {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+                script:
+                "echo hello"
+            }
+            '''
+
+        when:
+        def cmd = new CmdLint()
+        cmd.quiet = true
+        cmd.args = [dir.toFile().toString()]
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions) {
+                isQuiet() >> false
+                getAnsiLog() >> false
+            }
+        }
+        cmd.run()
+
+        then:
+        noExceptionThrown()
+        and:
+        !capture.toString().contains("Linting Nextflow code")
+        !capture.toString().contains("Linting:")
+        and:
+        capture.toString().contains("Nextflow linting complete")
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+    def 'should still show errors when progress is suppressed' () {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+
+                script:
+                """
+                ${
+                    params.is_paired_end
+                        ? "..."
+                        : "..."
+                }
+                """
+            }
+            '''
+
+        when:
+        def cmd = new CmdLint()
+        cmd.args = [dir.toFile().toString()]
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions) {
+                isQuiet() >> true
+                getAnsiLog() >> false
+            }
+        }
+        cmd.run()
+
+        then:
+        thrown(AbortOperationException)
+        and:
+        !capture.toString().contains("Linting Nextflow code")
+        !capture.toString().contains("Linting:")
+        and:
+        capture.toString().contains("Error")
+        capture.toString().contains("Unexpected input")
+        capture.toString().contains("Nextflow linting complete")
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
 }