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

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

@@ -26,8 +26,8 @@ import groovyx.gpars.dataflow.DataflowVariable
 import groovyx.gpars.dataflow.DataflowWriteChannel
 import nextflow.Channel
 /**
- * Operator for combining many source channels into a single channel,
- * with the option to only merge channels that are not marked as "iterators".
+ * Operator for merging many source channels into a single channel,
+ * with the option to combine channels that are marked as "iterators".
  *
  * @see ProcessDef#collectInputs(Object[])
  *
@@ -41,12 +41,26 @@ class CombineManyOp {
 
     private List<Integer> iterators
 
+    /**
+     * List of queues to receive values from source channels.
+     */
     private List<List> queues = []
 
+    /**
+     * Mask of source channels that are singletons.
+     */
     private List<Boolean> singletons
 
+    /**
+     * True when all source channels are singletons and therefore
+     * the operator should emit a singleton channel.
+     */
     private boolean emitSingleton
 
+    /**
+     * True when all source channels are iterators and therefore
+     * the operator should simply emit the combinations.
+     */
     private boolean emitCombination
 
     private transient List<List> combinations

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

@@ -28,15 +28,28 @@ import nextflow.util.LazyHelper
 @CompileStatic
 class ProcessFileInput implements PathArityAware {
 
+    /**
+     * Lazy expression (e.g. lazy var, closure, GString) which
+     * defines which files to stage in terms of the task inputs.
+     * It is evaluated for each task against the task context.
+     */
     private Object value
 
+    /**
+     * Optional name which, if specified, will be added to the task
+     * context as an escape-aware list of paths.
+     */
     private String name
 
     /**
      * Flag to support legacy `file` input.
      */
     private boolean pathQualifier
 
+    /**
+     * File pattern which defines how the input files should be named
+     * when they are staged into a task directory.
+     */
     private Object filePattern
 
     ProcessFileInput(Object value, String name, boolean pathQualifier, Map<String,?> opts) {

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

@@ -35,6 +35,11 @@ import nextflow.util.LazyHelper
 @CompileStatic
 class ProcessFileOutput implements PathArityAware {
 
+    /**
+     * Lazy expression (e.g. lazy var, closure, GString) which
+     * defines which files to unstage from the task directory.
+     * It will be evaluated for each task against the task directory.
+     */
     private Object target
 
     /**

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

@@ -32,8 +32,16 @@ import nextflow.extension.ToListOp
 @CompileStatic
 class ProcessInput implements Cloneable {
 
+    /**
+     * Parameter name under which the input value for each task
+     * will be added to the task context.
+     */
     private String name
 
+    /**
+     * Input channel which is created when the process is invoked
+     * in a workflow.
+     */
     private DataflowReadChannel channel
 
     /**

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

@@ -28,12 +28,31 @@ class ProcessInputs implements List<ProcessInput>, Cloneable {
     @Delegate
     private List<ProcessInput> params = []
 
+    /**
+     * Input variables which will be evaluated for each task
+     * in terms of the task inputs and added to the task context.
+     */
     private Map<String,?> vars = [:]
 
+    /**
+     * Environment variables which will be evaluated for each
+     * task against the task context and added to the task
+     * environment.
+     */
     private Map<String,?> env = [:]
 
+    /**
+     * Input files which will be evaluated for each task
+     * against the task context and staged into the task
+     * directory.
+     */
     private List<ProcessFileInput> files = []
 
+    /**
+     * Lazy expression which will be evaluated for each task
+     * against the task context and provided as the standard
+     * input to the task.
+     */
     Object stdin
 
     @Override

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

@@ -32,16 +32,41 @@ import nextflow.util.LazyHelper
 @CompileStatic
 class ProcessOutput implements Cloneable {
 
+    /**
+     * List of declared outputs of the parent process.
+     */
     private ProcessOutputs declaredOutputs
 
+    /**
+     * Lazy expression (e.g. lazy var, closure, GString) which
+     * defines the output value in terms of the task context,
+     * including environment variables, files, and standard output.
+     * It will be evaluated for each task after it is executed. 
+     */
     private Object target
 
+    /**
+     * Optional parameter name under which the output channel
+     * is made available in the process outputs (i.e. `.out`).
+     */
     private String name
 
+    /**
+     * Optional channel topic which this output channel will
+     * be sent to.
+     */
     private String topic
 
+    /**
+     * When true, a task will not fail if any environment
+     * vars or files for this output are missing.
+     */
     private boolean optional
 
+    /**
+     * Output channel which is created when the process is invoked
+     * in a workflow.
+     */
     private DataflowWriteChannel channel
 
     ProcessOutput(ProcessOutputs declaredOutputs, Object target, Map<String,?> opts) {

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

@@ -30,8 +30,18 @@ class ProcessOutputs implements List<ProcessOutput>, Cloneable {
     @Delegate
     private List<ProcessOutput> params = []
 
+    /**
+     * Environment variables which will be exported from the
+     * task environment for each task and made available to
+     * process outputs.
+     */
     private Map<String,String> env = [:]
 
+    /**
+     * Output files which will be unstaged from the task
+     * directory for each task and made available to process
+     * outputs.
+     */
     private Map<String,ProcessFileOutput> files = [:]
 
     @Override

modules/nextflow/src/main/groovy/nextflow/util/LazyHelper.groovy

@@ -20,7 +20,7 @@ import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode
 import groovy.transform.ToString
 /**
- * Helper methods for lazy binding and resolution.
+ * Helper methods for lazy evaluation.
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  * @author Ben Sherman <bentshermann@gmail.com>
@@ -29,7 +29,7 @@ import groovy.transform.ToString
 class LazyHelper {
 
     /**
-     * Resolve a lazy value against a given binding.
+     * Evaluate a lazy expression against a given binding.
      *
      * @param binding
      * @param value
@@ -50,14 +50,14 @@ class LazyHelper {
 }
 
 /**
- * Interface for types that can be lazily resolved
+ * Interface for types that can be lazily evaluated
  */
 interface LazyAware {
     Object resolve(Object binding)
 }
 
 /**
- * A list that can be lazily resolved
+ * A list that can be lazily evaluated
  */
 @CompileStatic
 class LazyList implements LazyAware, List {
@@ -88,7 +88,7 @@ class LazyList implements LazyAware, List {
 }
 
 /**
- * A map whose values can be lazily resolved
+ * A map whose values can be lazily evaluated
  */
 @CompileStatic
 class LazyMap implements Map<String,Object> {
@@ -263,7 +263,7 @@ class LazyMap implements Map<String,Object> {
 }
 
 /**
- * A variable that can be lazily resolved
+ * A variable that can be lazily evaluated
  */
 @CompileStatic
 @EqualsAndHashCode