Update index file default for single file

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy

@@ -121,8 +121,10 @@ class PublishOp {
      * @param value
      */
     protected Object normalizePaths(value) {
-        if( value instanceof Path )
-            return List.of(normalizePath(value))
+        if( value instanceof Path ) {
+            final target = normalizePath(value)
+            return List.of(targetDir.relativize(target), target)
+        }
 
         if( value instanceof Collection ) {
             return value.collect { el ->

modules/nextflow/src/test/groovy/nextflow/script/OutputDslTest.groovy

@@ -70,7 +70,7 @@ class OutputDslTest extends Specification {
         target.resolve('foo/file1.txt').text == 'Hello'
         target.resolve('barbar/file2.txt').text == 'world'
         target.resolve('barbar/index.csv').text == """\
-            "${target}/barbar/file2.txt"
+            "file2.txt","${target}/barbar/file2.txt"
             """.stripIndent()
         and:
         1 * session.notifyFilePublish(target.resolve('foo/file1.txt'), file1)