Merge pull request #168 from common-workflow-language/extra_links

explictly link to the extra docs

Author: mr-c

_episodes/07-containers.md

@@ -53,6 +53,7 @@ hints:
   DockerRequirement:
     dockerPull: node:slim
 ~~~
+{: .source}
 
 `baseCommand: node` tells CWL that we will be running this command in a container. We 
 then need to specify some `hints` for how to find the container we want.  In this case we list 
@@ -62,7 +63,6 @@ the name of the container image (you can even specify the tag, which is good ide
 best practises when using containers for reproducible research). In this case we have
 used a container called `node:slime`.
 
-{: .source}
 
 Provide a "hello.js" and invoke `cwl-runner` providing the tool wrapper and the
 input object on the command line:

_extras/miscellaneous.md

@@ -136,7 +136,7 @@ along with
 [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)
 
 >   merge_nested
-
+>
 > The input must be an array consisting of exactly one entry for each input link.
 > If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list.
 
@@ -176,9 +176,11 @@ outputs:
 
 For example, the filename is `a space is here.txt` includes 3 space characters.
 
-> ERROR Workflow error, try again with --debug for more information:
->
-> Invalid filename: 'a space is here.txt' contains illegal characters
+```console
+ERROR Workflow error, try again with --debug for more information:
+
+Invalid filename: 'a space is here.txt' contains illegal characters
+```
 
 If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`.
 
@@ -249,4 +251,4 @@ If is not possible to change the input identifier, then you can use an alternati
 
 ```cwl
 valueFrom: $(inputs["sample-input"])
-```
+```

bin/lesson_check.py

@@ -33,8 +33,6 @@
     '%/CONTRIBUTING.md': False,
     '%/LICENSE.md': True,
     '%/README.md': False,
-    '%/_extras/discuss.md': True,
-    '%/_extras/guide.md': True,
     '%/index.md': True,
     '%/reference.md': True,
     '%/setup.md': True,

index.md

@@ -29,6 +29,11 @@ This guide will introduce you to writing tool wrappers and workflows using the C
 > * A CWL runner. It is recommended to start with the [reference implementation][cwltool-install]. The full list of CWL runners is on [the project homepage][cwl-runners-list].
 {: .prereq}
 
+You also may be interested in:
+1. [A quick tutorial for the subset of YAML used in CWL]({{ page.root }}{% link _extras/yaml.md %})
+2. [CWL Recommended Practices]({{ page.root }}{% link _extras/recommended-practices.md %})
+3. [Miscellaneous CWL tips]({{ page.root }}{% link _extras/miscellaneous.md %})
+
 [cwl-runners-list]: https://www.commonwl.org/#Implementations
 [cwltool-install]: https://github.com/common-workflow-language/cwltool#install
 [repo]: https://github.com/common-workflow-language/user-guide/issues