Merge branch 'main' into correct-broken-link

Author: swzCuroverse

.github/workflows/gh-pages.yaml

@@ -3,7 +3,7 @@ name: GitHub Pages sphinx deployment
 on:
   push:
     branches:
-      - main
+      - release
   workflow_dispatch:
 
 # NOTE: If you modify this file to install a package with pip or apt, please
@@ -17,7 +17,7 @@ jobs:
 
       - name: Install apt packages
         run: |
-          sudo apt-get install -y graphviz
+          sudo apt-get install -y graphviz tree
 
       - name: Set up Python
         uses: actions/setup-python@v4

.gitignore

@@ -9,8 +9,9 @@ _site
 .Rproj.user
 .Rhistory
 .RData
-
 _build/
+build/
 *.egg-info/
 
 src/_includes/cwl/**/output.txt
+venv/

.readthedocs.yaml

@@ -9,6 +9,7 @@ build:
     nodejs: "16"
   apt_packages:
     - graphviz
+    - tree
 
 sphinx:
   configuration: src/conf.py

CONTRIBUTING.md

@@ -102,7 +102,7 @@ in `Makefile`).
 python -m venv venv
 source venv/bin/activate
 # Install the dependencies in your virtual environment
-(venv) pip install -e .[all]
+(venv) python -mpip install .[all]
 # Create the HTML to visualize locally
 (venv) make html
 (venv) firefox _build/index.html

src/_includes/cwl/expressions/custom-functions.js

@@ -0,0 +1,18 @@
+/**
+ * Capitalize each word passed. Will split the text by spaces.
+ * For instance, given "hello world", it returns "Hello World".
+ *
+ * @param {String} message - The input message.
+ * @return {String} the message with each word with its initial letter capitalized.
+ */
+function capitalizeWords (message) {
+  if (message === undefined || message === null || typeof message !== 'string' || message.trim().length === 0) {
+    return '';
+  }
+  return message
+    .split(' ')
+    .map(function (token) {
+      return token.charAt(0).toUpperCase() + token.slice(1);
+    })
+    .join(' ');
+}

src/_includes/cwl/expressions/hello-world-expressionlib-external.cwl

@@ -0,0 +1,16 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+    expressionLib:
+      - { $include: custom-functions.js }
+
+baseCommand: echo
+
+inputs:
+  message:
+    type: string
+
+arguments: [$( capitalizeWords(inputs.message) )]
+
+outputs: []

src/_includes/cwl/expressions/hello-world-expressionlib-inline.cwl

@@ -0,0 +1,34 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+    expressionLib:
+      - |
+        /**
+         * Capitalize each word passed. Will split the text by spaces.
+         * For instance, given "hello world", it returns "Hello World".
+         *
+         * @param {String} message - The input message.
+         * @return {String} the message with each word with its initial letter capitalized.
+         */
+        function capitalizeWords (message) {
+          if (message === undefined || message === null || typeof message !== 'string' || message.trim().length === 0) {
+            return '';
+          }
+          return message
+            .split(' ')
+            .map(function (token) {
+              return token.charAt(0).toUpperCase() + token.slice(1);
+            })
+            .join(' ');
+        }
+
+baseCommand: echo
+
+inputs:
+  message:
+    type: string
+
+arguments: [$( capitalizeWords(inputs.message) )]
+
+outputs: []

src/_includes/cwl/expressions/hello-world-expressionlib.cwl

@@ -0,0 +1,27 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+    expressionLib:
+      - { $include: custom-functions.js }
+      - |
+        /**
+         * A merely illustrative example function that uses a function
+         * from the included custom-functions.js file to create a
+         * Hello World message.
+         *
+         * @param {Object} message - CWL document input message
+         */
+        var createHelloWorldMessage = function (message) {
+          return capitalizeWords(message);
+        };
+
+baseCommand: echo
+
+inputs:
+  message:
+    type: string
+
+arguments: [$( createHelloWorldMessage(inputs.message) )]
+
+outputs: []

src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl

@@ -0,0 +1,25 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+inputs:
+  file_format:
+    type:
+      - 'null'
+      - name: format_choices
+        type: enum
+        symbols:
+          - auto
+          - fasta
+          - fastq
+          - fasta.gz
+          - fastq.gz
+        inputBinding:
+          position: 0
+          prefix: '--format'
+outputs:
+  text_output:
+    type: string
+    outputBinding:
+      outputEval: $(inputs.file_format)
+
+baseCommand: 'true'

src/_includes/cwl/troubleshooting/troubleshooting-wf1-stepb-fixed.cwl

@@ -0,0 +1,48 @@
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  text:
+    type: string
+    default: 'Hello World'
+outputs:
+  reversed_message:
+    type: string
+    outputSource: step_b/reversed_message
+
+steps:
+  step_a:
+    run:
+      class: CommandLineTool
+      stdout: stdout.txt
+      inputs:
+        text: string
+      outputs:
+        step_a_stdout:
+          type: File
+          outputBinding:
+            glob: 'stdout.txt'
+      baseCommand: echo
+      arguments: [ '-n', '$(inputs.text)' ]
+    in:
+      text: text
+    out: [step_a_stdout]
+  step_b:
+    run:
+      class: CommandLineTool
+      stdout: stdout.txt
+      inputs:
+        step_a_stdout: File
+      outputs:
+        reversed_message:
+          type: string
+          outputBinding:
+            glob: stdout.txt
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: rev
+      arguments: [ $(inputs.step_a_stdout) ]
+    in:
+      step_a_stdout:
+        source: step_a/step_a_stdout
+    out: [reversed_message]