Named arguments for processes and workflows

modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy

@@ -516,8 +516,10 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
 
     /// input parameters
 
-    InParam _in_val( obj ) {
-        new ValueInParam(this).bind(obj)
+    InParam _in_val( Map opts=null, Object obj ) {
+        new ValueInParam(this)
+                .setOptions(opts)
+                .bind(obj)
     }
 
     InParam _in_file( obj ) {

modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy

@@ -158,26 +158,46 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
 
     String getType() { 'process' }
 
-    private String missMatchErrMessage(String name, int expected, int actual) {
-        final ch = expected > 1 ? "channels" : "channel"
-        return "Process `$name` declares ${expected} input ${ch} but ${actual} were specified"
-    }
-
     @Override
     Object run(Object[] args) {
         // initialise process config
         initialize()
 
-        // get params 
-        final params = ChannelOut.spread(args)
-        // sanity check
-        if( params.size() != declaredInputs.size() )
-            throw new ScriptRuntimeException(missMatchErrMessage(processName, declaredInputs.size(), params.size()))
+        // separate named args and positional args
+        def namedArgs = [:]
+        def indexArgs = ChannelOut.spread(args)
+        if( !indexArgs.isEmpty() && indexArgs[0] instanceof Map )
+            namedArgs = indexArgs.remove(0) as Map
+
+        log.debug("named args: ${namedArgs}, positional args: ${indexArgs}")
+
+        // set named args
+        def names = namedArgs.keySet().collect()
+        def remainingInputs = []
+
+        for( def input : declaredInputs ) {
+            final inParam = (BaseInParam)input
+            final name = inParam.channelTakeName ?: inParam.name
+
+            if( name && namedArgs.containsKey(name) ) {
+                inParam.setFrom(namedArgs[name])
+                inParam.init()
+                names.remove(name)
+            }
+            else
+                remainingInputs << inParam
+        }
+
+        if( !names.isEmpty() )
+            throw new ScriptRuntimeException("Process `$name` was invoked with invalid named arguments: ${names.join(', ')}")
+
+        // set positional args
+        if( indexArgs.size() != remainingInputs.size() )
+            throw new ScriptRuntimeException("Process `$name` was invoked with ${indexArgs.size()} positional argument(s) but ${remainingInputs.size()} were expected")
 
-        // set input channels
-        for( int i=0; i<params.size(); i++ ) {
-            final inParam = (declaredInputs[i] as BaseInParam)
-            inParam.setFrom(params[i])
+        for( int i = 0; i < indexArgs.size(); i++ ) {
+            final inParam = (BaseInParam)remainingInputs[i]
+            inParam.setFrom(indexArgs[i])
             inParam.init()
         }
 

modules/nextflow/src/main/groovy/nextflow/script/WorkflowDef.groovy

@@ -125,16 +125,41 @@ class WorkflowDef extends BindableDef implements ChainableDef, IterableDef, Exec
 
 
     protected void collectInputs(Binding context, Object[] args) {
-        final params = ChannelOut.spread(args)
-        if( params.size() != declaredInputs.size() ) {
+        // separate named args and positional args
+        def namedArgs = [:]
+        def indexArgs = ChannelOut.spread(args)
+        if( !indexArgs.isEmpty() && indexArgs[0] instanceof Map )
+            namedArgs = indexArgs.remove(0) as Map
+
+        log.debug("named args: ${namedArgs}, positional args: ${indexArgs}")
+
+        // set named args
+        def names = namedArgs.keySet().collect()
+        def remainingInputs = new ArrayList<String>()
+
+        for( String name : declaredInputs ) {
+            if( name && namedArgs.containsKey(name) ) {
+                context.setProperty( name, namedArgs[name] )
+                names.remove(name)
+            }
+            else
+                remainingInputs << name
+        }
+
+        if( !names.isEmpty() ) {
+            final prefix = name ? "Workflow `$name`" : "Main workflow"
+            throw new IllegalArgumentException("$prefix was invoked with invalid named arguments: ${names.join(', ')}")
+        }
+
+        // set positional args
+        if( indexArgs.size() != remainingInputs.size() ) {
             final prefix = name ? "Workflow `$name`" : "Main workflow"
-            throw new IllegalArgumentException("$prefix declares ${declaredInputs.size()} input channels but ${params.size()} were given")
+            throw new IllegalArgumentException("$prefix was invoked with ${indexArgs.size()} positional argument(s) but ${remainingInputs.size()} were expected")
         }
 
-        // attach declared inputs with the invocation arguments
-        for( int i=0; i< declaredInputs.size(); i++ ) {
-            final name = declaredInputs[i]
-            context.setProperty( name, params[i] )
+        for( int i = 0; i < indexArgs.size(); i++ ) {
+            final name = remainingInputs[i]
+            context.setProperty( name, indexArgs[i] )
         }
     }
 

modules/nextflow/src/main/groovy/nextflow/script/params/BaseInParam.groovy

@@ -27,6 +27,7 @@ import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
 import nextflow.script.ProcessConfig
 import nextflow.script.TokenVar
+import nextflow.util.ConfigHelper
 /**
  * Model a process generic input parameter
  *
@@ -47,6 +48,8 @@ abstract class BaseInParam extends BaseParam implements InParam {
      */
     private inChannel
 
+    String channelTakeName
+
     /**
      * @return The input channel instance used by this parameter to receive the process inputs
      */
@@ -236,4 +239,19 @@ abstract class BaseInParam extends BaseParam implements InParam {
         return value
     }
 
+    BaseInParam setTake( value ) {
+        if( isNestedParam() )
+            throw new IllegalArgumentException("Input `take` option is not allowed in tuple components")
+        if( !value )
+            throw new IllegalArgumentException("Missing input `take` name")
+        if( !ConfigHelper.isValidIdentifier(value) ) {
+            final msg = "Input take '$value' is not a valid name -- Make sure it starts with an alphabetic or underscore character and it does not contain any blank, dot or other special characters"
+            if( NF.strictMode )
+                throw new IllegalArgumentException(msg)
+            log.warn(msg)
+        }
+        this.channelTakeName = value
+        return this
+    }
+
 }

modules/nextflow/src/main/groovy/nextflow/script/params/InParam.groovy

@@ -42,4 +42,6 @@ interface InParam extends Cloneable {
 
     def decodeInputs( List values )
 
+    String getChannelTakeName()
+
 }

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

@@ -359,7 +359,7 @@ class ScriptDslTest extends Dsl2Spec {
 
         then:
         def err = thrown(ScriptRuntimeException)
-        err.message == 'Process `bar` declares 1 input channel but 0 were specified'
+        err.message == 'Process `bar` was invoked with 0 positional argument(s) but 1 were expected'
     }
 
     def 'should report error accessing undefined out/a' () {
@@ -451,7 +451,7 @@ class ScriptDslTest extends Dsl2Spec {
 
         then:
         def err = thrown(ScriptRuntimeException)
-        err.message == "Process `bar` declares 1 input channel but 0 were specified"
+        err.message == "Process `bar` was invoked with 0 positional argument(s) but 1 were expected"
     }
 
     def 'should report error accessing undefined out/e' () {

tests/process-named-inputs.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+process foo {
+  input:
+    val bar
+    val baz
+  output: 
+    stdout
+
+  script:
+    """
+    echo $bar
+    echo $baz
+    """
+}
+
+
+workflow foo_wrapper {
+  take:
+    bar
+    baz
+  main:
+    foo(bar: bar, baz: baz)
+  emit:
+    foo.out
+}
+
+
+workflow {
+  foo_wrapper(bar: 'bar', baz: 'baz')
+    | view
+}