Fixed Staging input files in a subfolder changes their names when the…

…y are symlinks #292
nextflow-io · Mar 6, 2017 · e6fc342 · e6fc342
1 parent d4fe0a0
commit e6fc342
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/src/main/groovy/nextflow/processor/TaskProcessor.groovy b/src/main/groovy/nextflow/processor/TaskProcessor.groovy
@@ -1613,7 +1613,7 @@ class TaskProcessor {
         if( name.endsWith('/*') ) {
             final p = name.lastIndexOf('/')
             final dir = name.substring(0,p)
-            return files.collect { it.withName("${dir}/${it.storePath.name}") }
+            return files.collect { it.withName("${dir}/${it.stageName}") }
         }
 
         // no wildcards in the file name

diff --git a/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy b/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy
@@ -261,6 +261,13 @@ class TaskProcessorTest extends Specification {
         list1 *. stageName == ['dir/file.fa']
         list2 *. stageName == ['dir/file_1.fa', 'dir/file_2.fa', 'dir/file_3.fa']
 
+        when:
+        list1 = processor.expandWildcards('dir/*', [FileHolder.get('file.fa')])
+        list2 = processor.expandWildcards('dir/*', [FileHolder.get('titi.fa'), FileHolder.get('file.fq', 'toto.fa')])
+        then:
+        list1 *. stageName == ['dir/file.fa']
+        list2 *. stageName == ['dir/titi.fa', 'dir/toto.fa']
+
     }