From 2ab488362df7812a2326848afeeea836b0b10c44 Mon Sep 17 00:00:00 2001
From: Rob Syme <rob.syme@gmail.com>
Date: Thu, 11 Dec 2025 14:10:29 -0500
Subject: [PATCH] Fix leading **/ glob to match zero-or-more directories
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Java's glob pattern `**/foo` requires at least one directory component
before `foo`, but users expect it to also match `foo` at the root level.

This change transforms leading `**/` patterns to `{,**/}` which means
"either nothing OR any number of directories", correctly matching:
- `foo` (zero directories)
- `bar/foo` (one directory)
- `bar/baz/foo` (multiple directories)

This fixes issues where `files("path/**/subdir/*.txt")` would fail to
find files in `path/subdir/` while finding files in `path/x/subdir/`.

Fixes #5948

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Signed-off-by: Rob Syme <rob.syme@gmail.com>
---
 .../src/main/nextflow/file/FileHelper.groovy  |  8 +++-
 .../test/nextflow/file/FileHelperTest.groovy  | 42 +++++++++++++++++++
 2 files changed, 49 insertions(+), 1 deletion(-)

diff --git a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
index 83df9c6034..382bc6c44e 100644
--- a/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
+++ b/modules/nf-commons/src/main/nextflow/file/FileHelper.groovy
@@ -859,7 +859,13 @@ class FileHelper {
         final syntax = options.syntax ?: 'glob'
         final relative = options.relative == true
 
-        final matcher = getPathMatcherFor("$syntax:${filePattern}", folder.fileSystem)
+        // Transform leading ** to match zero-or-more directories (not just one-or-more)
+        // Java's glob ** at pattern start requires at least one directory component,
+        // but users expect **/foo to also match foo at the root level
+        final adjustedPattern = filePattern.startsWith('**/')
+            ? "{,**/}" + filePattern.substring(3)
+            : filePattern
+        final matcher = getPathMatcherFor("$syntax:${adjustedPattern}", folder.fileSystem)
         final singleParam = action.getMaximumNumberOfParameters() == 1
 
         Files.walkFileTree(folder, walkOptions, Integer.MAX_VALUE, new SimpleFileVisitor<Path>() {
diff --git a/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy b/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
index 7846caadc5..5364b492f3 100644
--- a/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
+++ b/modules/nf-commons/src/test/nextflow/file/FileHelperTest.groovy
@@ -624,6 +624,48 @@ class FileHelperTest extends Specification {
 
     }
 
+    def 'should match files at root and subdirectories with double-star glob'() {
+        // Tests that **/ pattern matches files at the root level (zero directories)
+        // as well as files in subdirectories (one or more directories)
+        // See: https://github.com/nextflow-io/nextflow/issues/5948
+
+        given:
+        def folder = Files.createTempDirectory('test')
+
+        // Create files at root level
+        folder.resolve('data.bin').text = 'root data'
+        folder.resolve('other.txt').text = 'other file'
+
+        // Create files in subdirectory
+        folder.resolve('subdir').mkdir()
+        folder.resolve('subdir').resolve('data.bin').text = 'subdir data'
+
+        // Create files in nested subdirectory
+        folder.resolve('subdir').resolve('nested').mkdir()
+        folder.resolve('subdir').resolve('nested').resolve('data.bin').text = 'nested data'
+
+        when: 'using **/ pattern should match files at all levels including root'
+        def result = []
+        FileHelper.visitFiles(folder, '**/data.bin', relative: true) { result << it.toString() }
+
+        then: 'files at root AND in subdirectories are matched'
+        result.sort() == ['data.bin', 'subdir/data.bin', 'subdir/nested/data.bin']
+
+        when: 'using **/ with intermediate directory should also match at all levels'
+        result = []
+        folder.resolve('InterOp').mkdir()
+        folder.resolve('InterOp').resolve('metrics.bin').text = 'root interop'
+        folder.resolve('subdir').resolve('InterOp').mkdir()
+        folder.resolve('subdir').resolve('InterOp').resolve('metrics.bin').text = 'subdir interop'
+        FileHelper.visitFiles(folder, '**/InterOp/*.bin', relative: true) { result << it.toString() }
+
+        then: 'InterOp directories at root AND in subdirectories are matched'
+        result.sort() == ['InterOp/metrics.bin', 'subdir/InterOp/metrics.bin']
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
 
     def 'should copy file path to foreign file system' () {