Add -files-from option to lint command to avoid ARG_MAX limit

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

@@ -17,6 +17,7 @@
 package nextflow.cli
 
 import java.nio.file.Path
+import java.nio.file.Files
 import java.time.Instant
 import java.time.ZoneOffset
 import java.time.format.DateTimeFormatter
@@ -58,6 +59,12 @@ class CmdLint extends CmdBase {
     @Parameter(description = 'List of paths to lint')
     List<String> args = []
 
+    @Parameter(
+        names = ['-files-from'],
+        description = 'Read list of paths to lint from file (one per line, use - for stdin)'
+    )
+    String filesFrom
+
     @Parameter(
         names = ['-exclude'],
         description = 'File pattern to exclude from error checking (can be specified multiple times)'
@@ -112,6 +119,20 @@ class CmdLint extends CmdBase {
 
     @Override
     void run() {
+        // Read paths from --files-from if specified
+        if( filesFrom ) {
+            if( args == null )
+                args = []
+            final lines = filesFrom == '-'
+                ? new BufferedReader(new InputStreamReader(System.in)).readLines()
+                : Files.readAllLines(Path.of(filesFrom))
+            for( final line : lines ) {
+                final trimmed = line.trim()
+                if( trimmed )
+                    args.add(trimmed)
+            }
+        }
+
         if( !args )
             throw new AbortOperationException("Error: No input files were specified")
 

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

@@ -81,4 +81,110 @@ class CmdLintTest extends Specification {
         dir?.deleteDir()
     }
 
+    def 'should read files from --files-from option' () {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+
+                script:
+                """
+                ${
+                    params.is_paired_end
+                        ? "..."
+                        : "..."
+                }
+                """
+            }
+            '''
+
+        def fileList = dir.resolve('filelist.txt')
+        fileList.text = dir.resolve('main.nf').toString() + '\n'
+
+        when:
+        def cmd = new CmdLint()
+        cmd.filesFrom = fileList.toFile().toString()
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions)
+        }
+        cmd.run()
+
+        then:
+        thrown(AbortOperationException)
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+    def 'should combine --files-from with positional args' () {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+
+        dir.resolve('main.nf').text = '''\
+            process HELLO {
+
+                script:
+                """
+                ${
+                    params.is_paired_end
+                        ? "..."
+                        : "..."
+                }
+                """
+            }
+            '''
+
+        dir.resolve('nextflow.config').text = '''\
+            process {
+                withLabel:
+                'bambino' {
+                    container = "..."
+                }
+            }
+            '''
+
+        def fileList = dir.resolve('filelist.txt')
+        fileList.text = dir.resolve('nextflow.config').toString() + '\n'
+
+        when:
+        def cmd = new CmdLint()
+        cmd.args = [dir.resolve('main.nf').toString()]
+        cmd.filesFrom = fileList.toFile().toString()
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions)
+        }
+        cmd.run()
+
+        then:
+        thrown(AbortOperationException)
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
+    def 'should throw error when --files-from file is empty' () {
+
+        given:
+        def dir = Files.createTempDirectory('test')
+        def fileList = dir.resolve('filelist.txt')
+        fileList.text = '\n'
+
+        when:
+        def cmd = new CmdLint()
+        cmd.filesFrom = fileList.toFile().toString()
+        cmd.launcher = Mock(Launcher) {
+            getOptions() >> Mock(CliOptions)
+        }
+        cmd.run()
+
+        then:
+        thrown(AbortOperationException)
+
+        cleanup:
+        dir?.deleteDir()
+    }
+
 }