Fixing changes in README

broadinstitute · Dec 9, 2016 · d264e3b · d264e3b
1 parent 55441ad
commit d264e3b
Showing 1 changed file with 78 additions and 0 deletions.
diff --git a/README.md b/README.md
@@ -22,6 +22,7 @@ A [Workflow Management System](https://en.wikipedia.org/wiki/Workflow_management
   * [server](#server)
   * [version](#version)
 * [Getting Started with WDL](#getting-started-with-wdl)
+  * [WDL Support](#wdl-support)
 * [Configuring Cromwell](#configuring-cromwell)
   * [Workflow Submission](#workflow-submission)
   * [Database](#database)
@@ -298,6 +299,83 @@ Returns the version of Cromwell engine.
 
 For many examples on how to use WDL see [the WDL site](https://github.com/broadinstitute/wdl#getting-started-with-wdl)
 
+## WDL Support
+
+:pig2: Cromwell supports the following subset of WDL features:
+
+* [Language Specification](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#language-specification)
+  * [Whitespace, Strings, Identifiers, Constants](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#whitespace-strings-identifiers-constants)
+  * [Types](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#types)
+  * [Fully Qualified Names & Namespaced Identifiers](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#fully-qualified-names--namespaced-identifiers)
+  * [Declarations](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#declarations)
+  * [Expressions](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#expressions)
+  * [Operator Precedence Table](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#operator-precedence-table)
+  * [Member Access](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#member-access)
+  * [Map and Array Indexing](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#map-and-array-indexing)
+  * [Function Calls](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#function-calls)
+  * [Array Literals](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#array-literals)
+  * [Map Literals](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#map-literals)
+* [Document](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#document)
+* [Task Definition](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#task-definition)
+  * [Sections](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#sections)
+  * [Command Section](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#command-section)
+    * [Command Parts](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#command-parts)
+    * [Command Part Options](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#command-part-options)
+      * [sep](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#sep)
+      * [true and false](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#true-and-false)
+      * [default](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#default)
+    * [Alternative heredoc syntax](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#alternative-heredoc-syntax)
+    * [Stripping Leading Whitespace](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#stripping-leading-whitespace)
+  * [Outputs Section](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs-section)
+  * [String Interpolation](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#string-interpolation)
+  * [Runtime Section](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#runtime-section)
+    * [docker](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#docker)
+    * [memory](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#memory)
+  * [Parameter Metadata Section](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#parameter-metadata-section)
+  * [Metadata Section](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#metadata-section)
+* [Workflow Definition](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#workflow-definition)
+  * [Call Statement](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#call-statement)
+    * [Sub Workflows](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#sub-workflows)
+  * [Scatter](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#scatter)
+  * [Outputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#outputs)
+* [Namespaces](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#namespaces)
+* [Scope](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#scope)
+* [Optional Parameters & Type Constraints](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#optional-parameters--type-constraints)
+  * [Prepending a String to an Optional Parameter](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#prepending-a-string-to-an-optional-parameter)
+* [Scatter / Gather](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#scatter--gather)
+* [Variable Resolution](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#variable-resolution)
+  * [Task-Level Resolution](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#task-level-resolution)
+  * [Workflow-Level Resolution](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#workflow-level-resolution)
+* [Computing Inputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#computing-inputs)
+  * [Task Inputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#task-inputs)
+  * [Workflow Inputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#workflow-inputs)
+  * [Specifying Workflow Inputs in JSON](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#specifying-workflow-inputs-in-json)
+* [Type Coercion](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#type-coercion)
+* [Standard Library](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#standard-library)
+  * [File stdout()](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#file-stdout)
+  * [File stderr()](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#file-stderr)
+  * [Array\[String\] read_lines(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#arraystring-read_linesstringfile)
+  * [Array\[Array\[String\]\] read_tsv(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#arrayarraystring-read_tsvstringfile)
+  * [Map\[String, String\] read_map(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#mapstring-string-read_mapstringfile)
+  * [Int read_int(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#int-read_intstringfile)
+  * [String read_string(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#string-read_stringstringfile)
+  * [Float read_float(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#float-read_floatstringfile)
+  * [Boolean read_boolean(String|File)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#boolean-read_booleanstringfile)
+  * [File write_lines(Array\[String\])](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#file-write_linesarraystring)
+  * [File write_tsv(Array\[Array\[String\]\])](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#file-write_tsvarrayarraystring)
+  * [File write_map(Map\[String, String\])](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#file-write_mapmapstring-string)
+  * [Float size(File, \[String\])](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#float-sizefile-string)
+  * [String sub(String, String, String)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#string-substring-string-string)
+  * [Array\[Int\] range(Int)](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#arrayint-rangeint)
+  * [Array\[Array\[X\]\] transpose(Array\[Array\[X\]\])](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#arrayarrayx-transposearrayarrayx)
+* [Data Types & Serialization](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#data-types--serialization)
+  * [Serialization of Task Inputs](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#serialization-of-task-inputs)
+    * [Primitive Types](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#primitive-types)
+    * [Compound Types](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#compound-types)
+      * [Array serialization](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#array-serialization)
+        * [Array serialization by expansion](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#array-serialization-by-expansion)
+        * [Array serialization using write_lines()](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md#array-serialization-using-write_lines)
+
 # Configuring Cromwell
 
 Cromwell's default configuration file is located at `src/main/resources/application.conf`.