update links to specifications in Introduction and Topics sections (#377)

Fienne · web-flow · commit 225478978301 · 2023-02-16T10:27:38.000-05:00
* update links to specifications in Introduction and Topics sections

* update links from http to https
diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md
@@ -138,9 +138,9 @@ The CWL specification allows for implementations to provide extra
 functionality and specify prerequisites to workflows through *requirements*.
 There are many requirements defined in the CWL specification, for instance:
 
-- `InlineJavascriptWorkflow` - enables JavaScript in expressions.
-- `SubworkflowFeatureRequirement` - enables nested workflows.
-- `InitialWorkDirRequirement` - controls staging files in the input directory.
+- [`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement) - enables JavaScript in expressions.
+- [`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement) - enables nested workflows.
+- [`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement) - controls staging files in the input directory.
 
 Some CWL runners may provide requirements that are not in the specification.
 For example, GPU requirements are supported in `cwltool` through the
diff --git a/src/topics/best-practices.md b/src/topics/best-practices.md
@@ -34,15 +34,15 @@ all are required.
   # other s: declarations
   ```
 
-  For more examples of providing metadata within CWL descriptions, see 
+  For more examples of providing metadata within CWL descriptions, see
   [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md).
 
 - Include [attribution information][license-example] for the author(s) of
   the CWL tool or workflow description. Use unambiguous identifiers like
   [ORCID][orcid].
 
 - In tool descriptions, list dependencies using short name(s) under
-  `SoftwareRequirement`.
+  [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement).
 
 - Include [SciCrunch][scicrunch] identifiers for dependencies in
   `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format.
@@ -53,7 +53,7 @@ all are required.
   `result`, `input`, `output`, and so forth.
 
 - In tool descriptions, include a list of version(s) of the tool that are
-  known to work with this description under `SoftwareRequirement`.
+  known to work with this description under [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement).
 
 - `format` should be specified for all input and output `File`s.
   Bioinformatics tools should use format identifiers from [EDAM][edam-example].
@@ -66,7 +66,7 @@ all are required.
 - Mark all input and output `File`s that are read from or written to in a
   streaming compatible way (only once, no random-access), as `streamable: true`.
 
-- Each `CommandLineTool` description should focus on a single operation
+- Each [`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool) description should focus on a single operation
   only, even if the (sub)command is capable of more. Don't overcomplicate your
   tool descriptions with options that you don't need or use.
 
diff --git a/src/topics/creating-files-at-runtime.md b/src/topics/creating-files-at-runtime.md
@@ -4,7 +4,7 @@ Sometimes you need to create a file on the fly from input parameters,
 such as tools that expect to read their input configuration from a file
 rather than the command line parameters, or need a small wrapper shell script.
 
-To generate such files, we can use the `InitialWorkDirRequirement`.
+To generate such files, we can use the [`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement).
 
 ```{literalinclude} /_includes/cwl/creating-files-at-runtime/createfile.cwl
 :language: cwl
diff --git a/src/topics/custom-types.md b/src/topics/custom-types.md
@@ -74,7 +74,7 @@ requirements:
 ```
 
 Note also that the author of this CWL description has also included
-`ResourceRequirement`s, specifying the minimum amount of RAM and number of cores
+[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s, specifying the minimum amount of RAM and number of cores
 required for the tool to run successfully, as well as details of the version of
 the software that the description was written for and other useful metadata.
 These features are discussed further in other chapters of this user guide.
diff --git a/src/topics/expression-tool.md b/src/topics/expression-tool.md
@@ -6,7 +6,7 @@ meant to be used as a way to isolate complex JavaScript expressions
 that need to operate on input data and produce some result as output.
 
 Similar to the command-line tool it requires `inputs` and `outputs`.
-But instead of `baseCommand`, it requires an `expression` attribute.
+But instead of `baseCommand`, it requires an [`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional)) attribute.
 
 % TODO: Fix the missing link the graph below. We cannot have
 %       it here as this file is included in two other files.
@@ -64,7 +64,7 @@ expression: |
 
 ```{note}
 
-We had to use an `InlineJavascriptRequirement` as our expression
+We had to use an [`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) as our expression
 contains a JavaScript call in `.toUpperCase()`. This means to tools
 using the expression tool that JavaScript is a requirement.
 ```
diff --git a/src/topics/expressions.md b/src/topics/expressions.md
@@ -1,7 +1,7 @@
 # Expressions
 
 If you need to manipulate input parameters, include the requirement
-`InlineJavascriptRequirement` and then anywhere a parameter reference is
+[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) and then anywhere a parameter reference is
 legal you can provide a fragment of Javascript that will be evaluated by
 the CWL runner.
 
@@ -80,7 +80,7 @@ only in certain fields.  These are:
     - From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)
       - `glob`
       - `outputEval`
-- From `Workflow`
+- From [`Workflow`](https://w3id.org/cwl/Workflow.html)
   - From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)
     - `format`
     - `secondaryFiles`
@@ -115,7 +115,7 @@ only in certain fields.  These are:
 
 ## Using External Libraries and Inline JavaScript Code with `expressionLib`
 
-The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute
+The requirement [`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) supports an `expressionLib` attribute
 that allows users to load external JavaScript files, or to provide inline JavaScript
 code.
 
diff --git a/src/topics/file-formats.md b/src/topics/file-formats.md
@@ -1,7 +1,7 @@
 # File Formats
 
-Tools and workflows can take `File` types as input and produce them as output.
-We also recommend indicating the format for `File` types. This helps document
+Tools and workflows can take [`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input and produce them as output.
+We also recommend indicating the format for [`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This helps document
 for others how to use your tool while allowing you to do some simple
 type-checking when creating parameter files.
 
diff --git a/src/topics/inputs.md b/src/topics/inputs.md
@@ -67,7 +67,7 @@ the tools aren't accidentally accessing files that were not explicitly
 specified
 ```
 
-The field `inputBinding` is optional and indicates whether and how the
+The field [`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding) is optional and indicates whether and how the
 input parameter should appear on the tool's command line.  If
 `inputBinding` is missing, the parameter does not appear on the command
 line.  Let's look at each example in detail.
diff --git a/src/topics/outputs.md b/src/topics/outputs.md
@@ -48,7 +48,7 @@ And now invoke `cwltool` with the tool description and the input object on the c
 :working-directory: src/_includes/cwl/outputs/
 ```
 
-The field `outputBinding` describes how to set the value of each
+The field [`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) describes how to set the value of each
 output parameter.
 
 ```cwl
@@ -59,12 +59,12 @@ outputs:
       glob: hello.txt
 ```
 
-The `glob` field consists of the name of a file in the output directory.
+The [`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) field consists of the name of a file in the output directory.
 If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`.
 
 ## Capturing Standard Output
 
-To capture a tool's standard output stream, add the `stdout` field with
+To capture a tool's standard output stream, add the [`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with
 the name of the file where the output stream should go.  Then add `type:
 stdout` on the corresponding output parameter.
 
diff --git a/src/topics/parameter-references.md b/src/topics/parameter-references.md
@@ -77,7 +77,7 @@ You can only use parameter references in certain fields.  These are:
     - From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)
       - `glob`
       - `outputEval`
-- From `Workflow`
+- From [`Workflow`](https://w3id.org/cwl/Workflow.html)
   - From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)
     - `format`
     - `secondaryFiles`
diff --git a/src/topics/specifying-software-requirements.md b/src/topics/specifying-software-requirements.md
@@ -2,7 +2,7 @@
 
 Often, tool descriptions will be written for a specific version of a software. To
 make it easier for others to use your descriptions, you can include a
-`SoftwareRequirement` field in the `hints` section.
+[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement) field in the `hints` section.
 This may also help to avoid confusion about which version of a tool the
 description was written for.
 
@@ -30,7 +30,7 @@ As well as a version number, a unique resource identifier (URI) for the tool is
 given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the
 [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking,
 and referring to scientific resources consistently. If you want to specify a
-tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the
+tool as a [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement), search for the tool on SciCrunch and use the
 RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer
 to the tool (via [identifiers.org][identifiers]) in the `specs` field of your
 requirement description. Other good choices, in order of preference, are to
diff --git a/src/topics/staging-input-files.md b/src/topics/staging-input-files.md
@@ -2,7 +2,7 @@
 
 Normally, input files are located in a read-only directory separate from
 the output directory.  This causes problems if the underlying tool expects to
-write its output files alongside the input file in the same directory.  You use `InitialWorkDirRequirement` to stage input files into the output directory.
+write its output files alongside the input file in the same directory.  You use [`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement) to stage input files into the output directory.
 In this example, we use a JavaScript expression to extract the base name of the
 input file from its leading directory path.
 
diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md
@@ -31,7 +31,7 @@ then print "Hello World" to the standard output.
 ```
 
 Before we run this, let's just break it down and see what some bits do.  Most of this
-has been explained in previous sections, the only part that is really new is the `dockerRequirement`
+has been explained in previous sections, the only part that is really new is the [`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)
 section.
 
 ```cwl
