diff --git a/_episodes/02-1st-example.md b/_episodes/02-1st-example.md
index e2431b49..7a087246 100644
--- a/_episodes/02-1st-example.md
+++ b/_episodes/02-1st-example.md
@@ -18,7 +18,7 @@ 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}
 
@@ -26,7 +26,7 @@ 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}
 
diff --git a/_episodes/03-input.md b/_episodes/03-input.md
index 963e594a..c143b1a1 100644
--- a/_episodes/03-input.md
+++ b/_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}
 
diff --git a/_episodes/04-output.md b/_episodes/04-output.md
index d30d72fa..9084f25d 100644
--- a/_episodes/04-output.md
+++ b/_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}
 
diff --git a/_episodes/05-stdout.md b/_episodes/05-stdout.md
index 9c046380..0bb19afb 100644
--- a/_episodes/05-stdout.md
+++ b/_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}
 
diff --git a/_episodes/06-params.md b/_episodes/06-params.md
index 68701aa2..7f5c3ec1 100644
--- a/_episodes/06-params.md
+++ b/_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}
 
diff --git a/_episodes/07-containers.md b/_episodes/07-containers.md
index f0bcff2d..239b4ff5 100644
--- a/_episodes/07-containers.md
+++ b/_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}
 
diff --git a/_episodes/08-arguments.md b/_episodes/08-arguments.md
index 374c4f80..0bb3bdad 100644
--- a/_episodes/08-arguments.md
+++ b/_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}
 
diff --git a/_episodes/09-array-inputs.md b/_episodes/09-array-inputs.md
index 97bb962d..af8e03cc 100644
--- a/_episodes/09-array-inputs.md
+++ b/_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}
 
diff --git a/_episodes/10-array-outputs.md b/_episodes/10-array-outputs.md
index dbcce1bd..56360710 100644
--- a/_episodes/10-array-outputs.md
+++ b/_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}
 
diff --git a/_episodes/11-records.md b/_episodes/11-records.md
index fb692df5..6724de52 100644
--- a/_episodes/11-records.md
+++ b/_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}
 
diff --git a/_episodes/12-env.md b/_episodes/12-env.md
index cba6f0e3..46cbeb66 100644
--- a/_episodes/12-env.md
+++ b/_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}
 
diff --git a/_episodes/13-expressions.md b/_episodes/13-expressions.md
index 15eea24f..5eb38e31 100644
--- a/_episodes/13-expressions.md
+++ b/_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}
 
diff --git a/_episodes/14-runtime.md b/_episodes/14-runtime.md
index f2d77fff..6449f889 100644
--- a/_episodes/14-runtime.md
+++ b/_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}
 
diff --git a/_episodes/15-staging.md b/_episodes/15-staging.md
index c3c0c303..f0f8fd10 100644
--- a/_episodes/15-staging.md
+++ b/_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}
 
diff --git a/_episodes/16-file-formats.md b/_episodes/16-file-formats.md
index 2a51cf4c..9c9ee1d2 100644
--- a/_episodes/16-file-formats.md
+++ b/_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}
 
diff --git a/_episodes/17-metadata.md b/_episodes/17-metadata.md
index 31e2983c..5e5f0c37 100644
--- a/_episodes/17-metadata.md
+++ b/_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}
 
diff --git a/_episodes/19-custom-types.md b/_episodes/19-custom-types.md
index 39fe3757..cb31b1ce 100644
--- a/_episodes/19-custom-types.md
+++ b/_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}
 
diff --git a/_episodes/20-software-requirements.md b/_episodes/20-software-requirements.md
index aabf9dc5..b34a52c9 100644
--- a/_episodes/20-software-requirements.md
+++ b/_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}
 
diff --git a/_episodes/21-1st-workflow.md b/_episodes/21-1st-workflow.md
index e886e0a5..eddae3fa 100644
--- a/_episodes/21-1st-workflow.md
+++ b/_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}
 
diff --git a/_episodes/22-nested-workflows.md b/_episodes/22-nested-workflows.md
index 41b448db..e3ddcfa3 100644
--- a/_episodes/22-nested-workflows.md
+++ b/_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}
 
diff --git a/_includes/cwl/1st-tool.cwl b/_includes/cwl/02-1st-example/1st-tool.cwl
similarity index 100%
rename from _includes/cwl/1st-tool.cwl
rename to _includes/cwl/02-1st-example/1st-tool.cwl
diff --git a/_includes/cwl/echo-job.yml b/_includes/cwl/02-1st-example/echo-job.yml
similarity index 100%
rename from _includes/cwl/echo-job.yml
rename to _includes/cwl/02-1st-example/echo-job.yml
diff --git a/_includes/cwl/inp-job.yml b/_includes/cwl/03-input/inp-job.yml
similarity index 100%
rename from _includes/cwl/inp-job.yml
rename to _includes/cwl/03-input/inp-job.yml
diff --git a/_includes/cwl/inp.cwl b/_includes/cwl/03-input/inp.cwl
similarity index 100%
rename from _includes/cwl/inp.cwl
rename to _includes/cwl/03-input/inp.cwl
diff --git a/_includes/cwl/tar-job.yml b/_includes/cwl/04-output/tar-job.yml
similarity index 100%
rename from _includes/cwl/tar-job.yml
rename to _includes/cwl/04-output/tar-job.yml
diff --git a/_includes/cwl/tar.cwl b/_includes/cwl/04-output/tar.cwl
similarity index 100%
rename from _includes/cwl/tar.cwl
rename to _includes/cwl/04-output/tar.cwl
diff --git a/_includes/cwl/05-stdout/echo-job.yml b/_includes/cwl/05-stdout/echo-job.yml
new file mode 100755
index 00000000..5329e737
--- /dev/null
+++ b/_includes/cwl/05-stdout/echo-job.yml
@@ -0,0 +1 @@
+message: Hello world!
diff --git a/_includes/cwl/stdout.cwl b/_includes/cwl/05-stdout/stdout.cwl
similarity index 100%
rename from _includes/cwl/stdout.cwl
rename to _includes/cwl/05-stdout/stdout.cwl
diff --git a/_includes/cwl/tar-param-job.yml b/_includes/cwl/06-params/tar-param-job.yml
similarity index 100%
rename from _includes/cwl/tar-param-job.yml
rename to _includes/cwl/06-params/tar-param-job.yml
diff --git a/_includes/cwl/tar-param.cwl b/_includes/cwl/06-params/tar-param.cwl
similarity index 100%
rename from _includes/cwl/tar-param.cwl
rename to _includes/cwl/06-params/tar-param.cwl
diff --git a/_includes/cwl/docker-job.yml b/_includes/cwl/07-containers/docker-job.yml
similarity index 100%
rename from _includes/cwl/docker-job.yml
rename to _includes/cwl/07-containers/docker-job.yml
diff --git a/_includes/cwl/docker.cwl b/_includes/cwl/07-containers/docker.cwl
similarity index 100%
rename from _includes/cwl/docker.cwl
rename to _includes/cwl/07-containers/docker.cwl
diff --git a/_includes/cwl/hello.js b/_includes/cwl/07-containers/hello.js
similarity index 100%
rename from _includes/cwl/hello.js
rename to _includes/cwl/07-containers/hello.js
diff --git a/_includes/cwl/Hello.java b/_includes/cwl/08-arguments/Hello.java
similarity index 100%
rename from _includes/cwl/Hello.java
rename to _includes/cwl/08-arguments/Hello.java
diff --git a/_includes/cwl/arguments-job.yml b/_includes/cwl/08-arguments/arguments-job.yml
similarity index 100%
rename from _includes/cwl/arguments-job.yml
rename to _includes/cwl/08-arguments/arguments-job.yml
diff --git a/_includes/cwl/arguments.cwl b/_includes/cwl/08-arguments/arguments.cwl
similarity index 100%
rename from _includes/cwl/arguments.cwl
rename to _includes/cwl/08-arguments/arguments.cwl
diff --git a/_includes/cwl/array-inputs-job.yml b/_includes/cwl/09-array-inputs/array-inputs-job.yml
similarity index 100%
rename from _includes/cwl/array-inputs-job.yml
rename to _includes/cwl/09-array-inputs/array-inputs-job.yml
diff --git a/_includes/cwl/array-inputs.cwl b/_includes/cwl/09-array-inputs/array-inputs.cwl
similarity index 100%
rename from _includes/cwl/array-inputs.cwl
rename to _includes/cwl/09-array-inputs/array-inputs.cwl
diff --git a/_includes/cwl/array-outputs-job.yml b/_includes/cwl/10-array-outputs/array-outputs-job.yml
similarity index 100%
rename from _includes/cwl/array-outputs-job.yml
rename to _includes/cwl/10-array-outputs/array-outputs-job.yml
diff --git a/_includes/cwl/array-outputs.cwl b/_includes/cwl/10-array-outputs/array-outputs.cwl
similarity index 100%
rename from _includes/cwl/array-outputs.cwl
rename to _includes/cwl/10-array-outputs/array-outputs.cwl
diff --git a/_includes/cwl/record-job1.yml b/_includes/cwl/11-records/record-job1.yml
similarity index 100%
rename from _includes/cwl/record-job1.yml
rename to _includes/cwl/11-records/record-job1.yml
diff --git a/_includes/cwl/record-job2.yml b/_includes/cwl/11-records/record-job2.yml
similarity index 100%
rename from _includes/cwl/record-job2.yml
rename to _includes/cwl/11-records/record-job2.yml
diff --git a/_includes/cwl/record-job3.yml b/_includes/cwl/11-records/record-job3.yml
similarity index 100%
rename from _includes/cwl/record-job3.yml
rename to _includes/cwl/11-records/record-job3.yml
diff --git a/_includes/cwl/record.cwl b/_includes/cwl/11-records/record.cwl
similarity index 100%
rename from _includes/cwl/record.cwl
rename to _includes/cwl/11-records/record.cwl
diff --git a/_includes/cwl/12-env/echo-job.yml b/_includes/cwl/12-env/echo-job.yml
new file mode 100755
index 00000000..5329e737
--- /dev/null
+++ b/_includes/cwl/12-env/echo-job.yml
@@ -0,0 +1 @@
+message: Hello world!
diff --git a/_includes/cwl/env.cwl b/_includes/cwl/12-env/env.cwl
similarity index 100%
rename from _includes/cwl/env.cwl
rename to _includes/cwl/12-env/env.cwl
diff --git a/_includes/cwl/empty.yml b/_includes/cwl/13-expressions/empty.yml
similarity index 100%
rename from _includes/cwl/empty.yml
rename to _includes/cwl/13-expressions/empty.yml
diff --git a/_includes/cwl/expression.cwl b/_includes/cwl/13-expressions/expression.cwl
similarity index 100%
rename from _includes/cwl/expression.cwl
rename to _includes/cwl/13-expressions/expression.cwl
diff --git a/_includes/cwl/createfile.cwl b/_includes/cwl/14-runtime/createfile.cwl
similarity index 100%
rename from _includes/cwl/createfile.cwl
rename to _includes/cwl/14-runtime/createfile.cwl
diff --git a/_includes/cwl/14-runtime/echo-job.yml b/_includes/cwl/14-runtime/echo-job.yml
new file mode 100755
index 00000000..5329e737
--- /dev/null
+++ b/_includes/cwl/14-runtime/echo-job.yml
@@ -0,0 +1 @@
+message: Hello world!
diff --git a/_includes/cwl/15-staging/Hello.java b/_includes/cwl/15-staging/Hello.java
new file mode 100644
index 00000000..6afc99f0
--- /dev/null
+++ b/_includes/cwl/15-staging/Hello.java
@@ -0,0 +1 @@
+public class Hello {}
diff --git a/_includes/cwl/15-staging/arguments-job.yml b/_includes/cwl/15-staging/arguments-job.yml
new file mode 100644
index 00000000..9e56989a
--- /dev/null
+++ b/_includes/cwl/15-staging/arguments-job.yml
@@ -0,0 +1,3 @@
+src:
+  class: File
+  path: Hello.java
diff --git a/_includes/cwl/linkfile.cwl b/_includes/cwl/15-staging/linkfile.cwl
similarity index 100%
rename from _includes/cwl/linkfile.cwl
rename to _includes/cwl/15-staging/linkfile.cwl
diff --git a/_includes/cwl/file-formats.bam b/_includes/cwl/16-file-formats/file-formats.bam
similarity index 100%
rename from _includes/cwl/file-formats.bam
rename to _includes/cwl/16-file-formats/file-formats.bam
diff --git a/_includes/cwl/metadata_example.cwl b/_includes/cwl/16-file-formats/metadata_example.cwl
similarity index 100%
rename from _includes/cwl/metadata_example.cwl
rename to _includes/cwl/16-file-formats/metadata_example.cwl
diff --git a/_includes/cwl/sample.yml b/_includes/cwl/16-file-formats/sample.yml
similarity index 100%
rename from _includes/cwl/sample.yml
rename to _includes/cwl/16-file-formats/sample.yml
diff --git a/_includes/cwl/metadata_example2.cwl b/_includes/cwl/17-metadata/metadata_example2.cwl
similarity index 100%
rename from _includes/cwl/metadata_example2.cwl
rename to _includes/cwl/17-metadata/metadata_example2.cwl
diff --git a/_includes/cwl/metadata_example3.cwl b/_includes/cwl/17-metadata/metadata_example3.cwl
similarity index 100%
rename from _includes/cwl/metadata_example3.cwl
rename to _includes/cwl/17-metadata/metadata_example3.cwl
diff --git a/_includes/cwl/InterProScan-apps.yml b/_includes/cwl/19-custom-types/InterProScan-apps.yml
similarity index 100%
rename from _includes/cwl/InterProScan-apps.yml
rename to _includes/cwl/19-custom-types/InterProScan-apps.yml
diff --git a/_includes/cwl/custom-types.cwl b/_includes/cwl/19-custom-types/custom-types.cwl
similarity index 100%
rename from _includes/cwl/custom-types.cwl
rename to _includes/cwl/19-custom-types/custom-types.cwl
diff --git a/_includes/cwl/custom-types.yml b/_includes/cwl/19-custom-types/custom-types.yml
similarity index 100%
rename from _includes/cwl/custom-types.yml
rename to _includes/cwl/19-custom-types/custom-types.yml
diff --git a/_includes/cwl/test_proteins.fasta b/_includes/cwl/19-custom-types/test_proteins.fasta
similarity index 100%
rename from _includes/cwl/test_proteins.fasta
rename to _includes/cwl/19-custom-types/test_proteins.fasta
diff --git a/_includes/cwl/20-software-requirements/custom-types.cwl b/_includes/cwl/20-software-requirements/custom-types.cwl
new file mode 100644
index 00000000..75d1b294
--- /dev/null
+++ b/_includes/cwl/20-software-requirements/custom-types.cwl
@@ -0,0 +1,67 @@
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: "InterProScan: protein sequence classifier"
+
+doc: |
+      Version 5.21-60 can be downloaded here:
+      https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload
+
+      Documentation on how to run InterProScan 5 can be found here:
+      https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
+
+requirements:
+  ResourceRequirement:
+    ramMin: 10240
+    coresMin: 3
+  SchemaDefRequirement:
+    types:
+      - $import: InterProScan-apps.yml
+
+hints:
+  SoftwareRequirement:
+    packages:
+      interproscan:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_005829" ]
+        version: [ "5.21-60" ]
+
+inputs:
+  proteinFile:
+    type: File
+    inputBinding:
+      prefix: --input
+  applications:
+    type: InterProScan-apps.yml#apps[]?
+    inputBinding:
+      itemSeparator: ','
+      prefix: --applications
+
+baseCommand: interproscan.sh
+
+arguments:
+ - valueFrom: $(inputs.proteinFile.nameroot).i5_annotations
+   prefix: --outfile
+ - valueFrom: TSV
+   prefix: --formats
+ - --disable-precalc
+ - --goterms
+ - --pathways
+ - valueFrom: $(runtime.tmpdir)
+   prefix: --tempdir
+
+
+outputs:
+  i5Annotations:
+    type: File
+    format: iana:text/tab-separated-values
+    outputBinding:
+      glob: $(inputs.proteinFile.nameroot).i5_annotations
+
+$namespaces:
+ iana: https://www.iana.org/assignments/media-types/
+ s: http://schema.org/
+$schemas:
+ - https://schema.org/docs/schema_org_rdfa.html
+
+s:license: "https://www.apache.org/licenses/LICENSE-2.0"
+s:copyrightHolder: "EMBL - European Bioinformatics Institute"
diff --git a/_includes/cwl/1st-workflow-job.yml b/_includes/cwl/21-1st-workflow/1st-workflow-job.yml
similarity index 100%
rename from _includes/cwl/1st-workflow-job.yml
rename to _includes/cwl/21-1st-workflow/1st-workflow-job.yml
diff --git a/_includes/cwl/1st-workflow.cwl b/_includes/cwl/21-1st-workflow/1st-workflow.cwl
similarity index 100%
rename from _includes/cwl/1st-workflow.cwl
rename to _includes/cwl/21-1st-workflow/1st-workflow.cwl
diff --git a/_includes/cwl/nestedworkflows.cwl b/_includes/cwl/22-nested-workflows/nestedworkflows.cwl
similarity index 100%
rename from _includes/cwl/nestedworkflows.cwl
rename to _includes/cwl/22-nested-workflows/nestedworkflows.cwl
diff --git a/_includes/cwl/createfile-job.yml b/_includes/cwl/createfile-job.yml
deleted file mode 100644
index 7f538871..00000000
--- a/_includes/cwl/createfile-job.yml
+++ /dev/null
@@ -1 +0,0 @@
-conf: hello
diff --git a/_includes/cwl/empty.json b/_includes/cwl/empty.json
deleted file mode 100644
index 0967ef42..00000000
--- a/_includes/cwl/empty.json
+++ /dev/null
@@ -1 +0,0 @@
-{}