Fix failing tests

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

docs/process-typed.md

@@ -75,7 +75,7 @@ process cat_opt {
     input: Path?
 
     stage:
-    stageAs 'input.txt', input
+    stageAs input, 'input.txt'
 
     output:
     stdout()

modules/nextflow/src/test/groovy/nextflow/script/dsl/ProcessDslV2Test.groovy

@@ -40,7 +40,7 @@ class ProcessDslV2Test extends Specification {
         dsl._input_('infile', Path, false)
         dsl._input_('x', String, false)
         dsl._input_('y', String, false)
-        dsl.stageAs('filename.fa', { infile })
+        dsl.stageAs({ -> infile }, 'filename.fa')
         dsl.stdin { y }
 
         then:
@@ -112,7 +112,7 @@ class ProcessDslV2Test extends Specification {
         dsl.memory '10 GB'
         dsl._input_('foo', String, false)
         dsl._input_('sample', Path, false)
-        dsl.stageAs('sample.txt', { sample })
+        dsl.stageAs({ -> sample }, 'sample.txt')
         dsl._output_('result', Path, { file('$file0') })
         dsl._unstage_files('$file0', 'result.txt')
 

modules/nf-lang/src/main/java/nextflow/script/control/ProcessToGroovyVisitorV2.java

@@ -120,7 +120,7 @@ private void visitProcessDirectives(Statement directives) {
     private void visitProcessStagers(Statement directives) {
         asDirectives(directives).forEach((call) -> {
             var arguments = asMethodCallArguments(call).stream()
-                .map(arg -> sgh.transformToLazy(arg))
+                .map(arg -> sgh.transformToLazy(arg, false))
                 .toList();
             call.setArguments(args(arguments));
         });

modules/nf-lang/src/main/java/nextflow/script/control/ScriptToGroovyHelper.java

@@ -21,6 +21,7 @@
 import java.util.Set;
 
 import org.codehaus.groovy.ast.CodeVisitorSupport;
+import org.codehaus.groovy.ast.Parameter;
 import org.codehaus.groovy.ast.Variable;
 import org.codehaus.groovy.ast.expr.ClosureExpression;
 import org.codehaus.groovy.ast.expr.Expression;
@@ -119,16 +120,23 @@ private static String asPropertyChain(PropertyExpression node) {
      * wrapping it in a closure if it references variables.
      *
      * @param node
+     * @param implicitParam
      */
-    public Expression transformToLazy(Expression node)  {
+    public Expression transformToLazy(Expression node, boolean implicitParam) {
         if( node instanceof ClosureExpression )
             return node;
         var vars = new VariableCollector().collect(node);
-        if( !vars.isEmpty() )
-            return closureX(null, stmt(node));
+        if( !vars.isEmpty() ) {
+            var parameters = implicitParam ? Parameter.EMPTY_ARRAY : null;
+            return closureX(parameters, stmt(node));
+        }
         return node;
     }
 
+    public Expression transformToLazy(Expression node) {
+        return transformToLazy(node, true);
+    }
+
     private class VariableCollector extends CodeVisitorSupport {
 
         private Set<Variable> vars;

modules/nf-lang/src/test/groovy/nextflow/script/formatter/ScriptFormatterTest.groovy

@@ -207,7 +207,7 @@ class ScriptFormatterTest extends Specification {
             nextflow.preview.types=true
 
             process hello{
-            debug(true) ; input: (id,infile):Tuple<String,Path> ; index:Path ; stage: stageAs('input.txt',infile) ; output: result=tuple(id,file('output.txt')) ; script: 'cat input.txt > output.txt'
+            debug(true) ; input: (id,infile):Tuple<String,Path> ; index:Path ; stage: stageAs(infile,'input.txt') ; output: result=tuple(id,file('output.txt')) ; script: 'cat input.txt > output.txt'
             }
             ''',
             '''\
@@ -221,7 +221,7 @@ class ScriptFormatterTest extends Specification {
                 index: Path
 
                 stage:
-                stageAs 'input.txt', infile
+                stageAs infile, 'input.txt'
 
                 output:
                 result = tuple(id, file('output.txt'))

tests/collect-tuple-typed.nf

@@ -32,8 +32,8 @@ process merge {
   (barcode, seq_ids, bam, bai): Tuple<String, Bag<String>, Bag<Path>, Bag<Path>>
 
   stage:
-  stageAs 'bam?', bam
-  stageAs 'bai?', bai
+  stageAs bam, 'bam?'
+  stageAs bai, 'bai?'
 
   script:
   """

tests/dynamic-filename-typed.nf

@@ -27,7 +27,7 @@ process foo {
   (name, txt): Tuple<String, Path>
 
   stage:
-  stageAs "${params.prefix}_${name}.txt", txt
+  stageAs txt, "${params.prefix}_${name}.txt"
 
   output:
   file("${params.prefix}_${name}.txt")

tests/nullable-path.nf

@@ -20,7 +20,7 @@ process bar {
     input: Path?
 
     stage:
-    stageAs 'input.txt', input
+    stageAs input, 'input.txt'
 
     output:
     stdout()