Categorize the examples for each section

_episodes/02-1st-example.md

@@ -18,15 +18,15 @@ The simplest "hello world" program.  This accepts one input parameter, writes a
 
 *1st-tool.cwl*
 ~~~
-{% include cwl/1st-tool.cwl %}
+{% include cwl/02-1st-example/1st-tool.cwl %}
 ~~~
 {: .source}
 
 Use a YAML or JSON object in a separate file to describe the input of a run:
 
 *echo-job.yml*
 ~~~
-{% include cwl/echo-job.yml %}
+{% include cwl/02-1st-example/echo-job.yml %}
 ~~~
 {: .source}
 

_episodes/03-input.md

@@ -29,14 +29,14 @@ types and appearing on the command line in different ways:
 *inp.cwl*
 
 ~~~
-{% include cwl/inp.cwl %}
+{% include cwl/03-input/inp.cwl %}
 ~~~
 {: .source}
 
 *inp-job.yml*
 
 ~~~
-{% include cwl/inp-job.yml %}
+{% include cwl/03-input/inp-job.yml %}
 ~~~
 {: .source}
 

_episodes/04-output.md

@@ -26,14 +26,14 @@ themselves, or come from examining the content of those files.
 *tar.cwl*
 
 ~~~
-{% include cwl/tar.cwl %}
+{% include cwl/04-output/tar.cwl %}
 ~~~
 {: .source}
 
 *tar-job.yml*
 
 ~~~
-{% include cwl/tar-job.yml %}
+{% include cwl/04-output/tar-job.yml %}
 ~~~
 {: .source}
 

_episodes/05-stdout.md

@@ -17,14 +17,14 @@ stdout` on the corresponding output parameter.
 *stdout.cwl*
 
 ~~~
-{% include cwl/stdout.cwl %}
+{% include cwl/05-stdout/stdout.cwl %}
 ~~~
 {: .source}
 
 *echo-job.yml*
 
 ~~~
-{% include cwl/echo-job.yml %}
+{% include cwl/05-stdout/echo-job.yml %}
 ~~~
 {: .source}
 

_episodes/06-params.md

@@ -19,14 +19,14 @@ fields.
 *tar-param.cwl*
 
 ~~~
-{% include cwl/tar-param.cwl %}
+{% include cwl/06-params/tar-param.cwl %}
 ~~~
 {: .source}
 
 *tar-param-job.yml*
 
 ~~~
-{% include cwl/tar-param-job.yml %}
+{% include cwl/06-params/tar-param-job.yml %}
 ~~~
 {: .source}
 

_episodes/07-containers.md

@@ -27,14 +27,14 @@ This example runs a simple Node.js script inside a Docker container.
 *docker.cwl*
 
 ~~~
-{% include cwl/docker.cwl %}
+{% include cwl/07-containers/docker.cwl %}
 ~~~
 {: .source}
 
 *docker-job.yml*
 
 ~~~
-{% include cwl/docker-job.yml %}
+{% include cwl/07-containers/docker-job.yml %}
 ~~~
 {: .source}
 

_episodes/08-arguments.md

@@ -28,14 +28,14 @@ instead.
 *arguments.cwl*
 
 ~~~
-{% include cwl/arguments.cwl %}
+{% include cwl/08-arguments/arguments.cwl %}
 ~~~
 {: .source}
 
 *arguments-job.yml*
 
 ~~~
-{% include cwl/arguments-job.yml %}
+{% include cwl/08-arguments/arguments-job.yml %}
 ~~~
 {: .source}
 

_episodes/09-array-inputs.md

@@ -24,14 +24,14 @@ data types that may appear in the array.
 *array-inputs.cwl*
 
 ~~~
-{% include cwl/array-inputs.cwl %}
+{% include cwl/09-array-inputs/array-inputs.cwl %}
 ~~~
 {: .source}
 
 *array-inputs-job.yml*
 
 ~~~
-{% include cwl/array-inputs-job.yml %}
+{% include cwl/09-array-inputs/array-inputs-job.yml %}
 ~~~
 {: .source}
 

_episodes/10-array-outputs.md

@@ -16,14 +16,14 @@ You can also capture multiple output files into an array of files using `glob`.
 *array-outputs.cwl*
 
 ~~~
-{% include cwl/array-outputs.cwl %}
+{% include cwl/10-array-outputs/array-outputs.cwl %}
 ~~~
 {: .source}
 
 *array-outputs-job.yml*
 
 ~~~
-{% include cwl/array-outputs-job.yml %}
+{% include cwl/10-array-outputs/array-outputs-job.yml %}
 ~~~
 {: .source}
 

_episodes/11-records.md

@@ -19,14 +19,14 @@ parameters together to describe these two conditions.
 *record.cwl*
 
 ~~~
-{% include cwl/record.cwl %}
+{% include cwl/11-records/record.cwl %}
 ~~~
 {: .source}
 
 *record-job1.yml*
 
 ~~~
-{% include cwl/record-job1.yml %}
+{% include cwl/11-records/record-job1.yml %}
 ~~~
 {: .source}
 
@@ -43,7 +43,7 @@ In the first example, you can't provide `itemA` without also providing `itemB`.
 *record-job2.yml*
 
 ~~~
-{% include cwl/record-job2.yml %}
+{% include cwl/11-records/record-job2.yml %}
 ~~~
 {: .source}
 
@@ -62,7 +62,7 @@ is added to the command line and `itemD` is ignored.
 *record-job3.yml*
 
 ~~~
-{% include cwl/record-job3.yml %}
+{% include cwl/11-records/record-job3.yml %}
 ~~~
 {: .source}
 

_episodes/12-env.md

@@ -19,14 +19,14 @@ the tool using `EnvVarRequirement`.
 *env.cwl*
 
 ~~~
-{% include cwl/env.cwl %}
+{% include cwl/12-env/env.cwl %}
 ~~~
 {: .source}
 
 *echo-job.yml*
 
 ~~~
-{% include cwl/echo-job.yml %}
+{% include cwl/12-env/echo-job.yml %}
 ~~~
 {: .source}
 

_episodes/13-expressions.md

@@ -27,7 +27,7 @@ See the [list of recommended practices][rec-practices].__
 *expression.cwl*
 
 ~~~
-{% include cwl/expression.cwl %}
+{% include cwl/13-expressions/expression.cwl %}
 ~~~
 {: .source}
 
@@ -37,7 +37,7 @@ job file:
 *empty.yml*
 
 ~~~
-{% include cwl/empty.yml %}
+{% include cwl/13-expressions/empty.yml %}
 ~~~
 {: .source}
 

_episodes/14-runtime.md

@@ -18,14 +18,14 @@ rather than the command line parameters.  To do this, use
 *createfile.cwl*
 
 ~~~
-{% include cwl/createfile.cwl %}
+{% include cwl/14-runtime/createfile.cwl %}
 ~~~
 {: .source}
 
 *echo-job.yml*
 
 ~~~
-{% include cwl/echo-job.yml %}
+{% include cwl/14-runtime/echo-job.yml %}
 ~~~
 {: .source}
 

_episodes/15-staging.md

@@ -21,14 +21,14 @@ input file from its leading directory path.
 *linkfile.cwl*
 
 ~~~
-{% include cwl/linkfile.cwl %}
+{% include cwl/15-staging/linkfile.cwl %}
 ~~~
 {: .source}
 
 *arguments-job.yml*
 
 ~~~
-{% include cwl/arguments-job.yml %}
+{% include cwl/15-staging/arguments-job.yml %}
 ~~~
 {: .source}
 

_episodes/16-file-formats.md

@@ -28,7 +28,7 @@ formats and warn you if there seem to be some obvious mismatches.
 *metadata_example.cwl*
 
 ~~~
-{% include cwl/metadata_example.cwl %}
+{% include cwl/16-file-formats/metadata_example.cwl %}
 ~~~
 {: .source}
 
@@ -42,15 +42,15 @@ parameterization.
 *sample.json*
 
 ~~~
-{% include cwl/sample.yml %}
+{% include cwl/16-file-formats/sample.yml %}
 ~~~
 {: .source}
 
-___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from [https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/file-formats.bam
-](https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/file-formats.bam) and can be downloaded e.g. via `wget`:
+___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from [https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam
+](https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam) and can be downloaded e.g. via `wget`:
 
 ~~~
-wget https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/file-formats.bam
+wget https://github.com/common-workflow-language/user_guide/raw/gh-pages/_includes/cwl/16-file-formats/file-formats.bam
 ~~~
 {: .source}
 

_episodes/17-metadata.md

@@ -26,7 +26,7 @@ and workflows. This example includes metadata allowing others to cite your tool.
 *metadata_example2.cwl*
 
 ~~~
-{% include cwl/metadata_example2.cwl %}
+{% include cwl/17-metadata/metadata_example2.cwl %}
 ~~~
 {: .source}
 
@@ -40,7 +40,7 @@ requirements in order to use the tool, and a few more metadata fields.
 *metadata_example3.cwl*
 
 ~~~
-{% include cwl/metadata_example3.cwl %}
+{% include cwl/17-metadata/metadata_example3.cwl %}
 ~~~
 {: .source}
 

_episodes/19-custom-types.md

@@ -27,14 +27,14 @@ It is a good example of a number of good practices in CWL.
 *custom-types.cwl*
 
 ~~~
-{% include cwl/custom-types.cwl %}
+{% include cwl/19-custom-types/custom-types.cwl %}
 ~~~
 {: .source}
 
 *custom-types.yml*
 
 ~~~
-{% include cwl/custom-types.yml %}
+{% include cwl/19-custom-types/custom-types.yml %}
 ~~~
 {: .source}
 
@@ -64,7 +64,7 @@ type from the imported `InterProScan-apps.yaml` file
 The contents of the YAML file describing the custom type are given below:
 
 ~~~
-{% include cwl/InterProScan-apps.yml %}
+{% include cwl/19-custom-types/InterProScan-apps.yml %}
 ~~~
 {: .source}
 

_episodes/20-software-requirements.md

@@ -19,7 +19,7 @@ This may also help to avoid confusion about which version of a tool the
 description was written for.
 
 ~~~
-{% include cwl/custom-types.cwl %}
+{% include cwl/20-software-requirements/custom-types.cwl %}
 ~~~
 {: .source}
 

_episodes/21-1st-workflow.md

@@ -20,7 +20,7 @@ compiles it.
 *1st-workflow.cwl*
 
 ~~~
-{% include cwl/1st-workflow.cwl %}
+{% include cwl/21-1st-workflow/1st-workflow.cwl %}
 ~~~
 {: .source}
 
@@ -29,7 +29,7 @@ Use a JSON object in a separate file to describe the input of a run:
 *1st-workflow-job.yml*
 
 ~~~
-{% include cwl/1st-workflow-job.yml %}
+{% include cwl/21-1st-workflow/1st-workflow-job.yml %}
 ~~~
 {: .source}
 

_episodes/22-nested-workflows.md

@@ -32,7 +32,7 @@ Here's an example workflow that uses our `1st-workflow.cwl` as a nested
 workflow:
 
 ~~~
-{% include cwl/nestedworkflows.cwl %}
+{% include cwl/22-nested-workflows/nestedworkflows.cwl %}
 ~~~
 {: .source}
 

_includes/cwl/05-stdout/echo-job.yml

@@ -0,0 +1 @@
+message: Hello world!

_includes/cwl/12-env/echo-job.yml

@@ -0,0 +1 @@
+message: Hello world!

_includes/cwl/14-runtime/echo-job.yml

@@ -0,0 +1 @@
+message: Hello world!

_includes/cwl/15-staging/Hello.java

@@ -0,0 +1 @@
+public class Hello {}

_includes/cwl/15-staging/arguments-job.yml

@@ -0,0 +1,3 @@
+src:
+  class: File
+  path: Hello.java