├── .github
    ├── assets
    │   └── readme-header.svg
    └── workflows
    │   └── docs.yml
├── .gitignore
├── .vitepress
    ├── config.mts
    └── theme
    │   ├── index.ts
    │   └── style.css
├── LICENSE
├── README.md
├── design-patterns
    ├── branch-and-merge
    │   ├── header.png
    │   └── index.md
    ├── conditional-statement
    │   ├── header.png
    │   └── index.md
    ├── linear-chaining
    │   ├── header.png
    │   └── index.md
    ├── multiple-io
    │   ├── header.png
    │   └── index.md
    ├── scatter-gather
    │   ├── header.png
    │   └── index.md
    └── task-aliasing
    │   ├── header.png
    │   └── index.md
├── getting-started
    ├── contributing.md
    ├── ecosystem.md
    ├── getting-help.md
    └── quickstart.md
├── index.md
├── language-guide
    ├── imports.md
    ├── structs.md
    ├── tasks.md
    ├── variables.md
    ├── versions.md
    └── workflows.md
├── overview.md
├── package-lock.json
├── package.json
├── pnpm-lock.yaml
├── public
    ├── favicon.ico
    ├── hero.svg
    └── logo-only.svg
└── reference
    ├── stdlib
        ├── file.md
        ├── numeric.md
        ├── string-array.md
        └── string.md
    └── upgrade-guide.md


/.github/workflows/docs.yml:
--------------------------------------------------------------------------------
 1 | name: Docs
 2 | 
 3 | on:
 4 |   push:
 5 |     branches:
 6 |       - main
 7 | 
 8 | permissions:
 9 |   contents: read
10 |   pages: write
11 |   id-token: write
12 | 
13 | concurrency:
14 |   group: "pages"
15 |   cancel-in-progress: false
16 | 
17 | jobs:
18 |   build:
19 |     runs-on: ubuntu-latest
20 |     steps:
21 |       - uses: actions/checkout@v4
22 |       - uses: actions/setup-node@v4
23 |         with:
24 |           node-version: "latest"
25 |       - run: npm install && npm run docs:build
26 |       - uses: actions/upload-pages-artifact@v3
27 |         with:
28 |           name: "WDL Documentation"
29 |           path: ".vitepress/dist"
30 |   deploy:
31 |     needs: build
32 |     if: success() && github.ref == 'refs/heads/main'
33 |     permissions:
34 |       pages: write
35 |       id-token: write
36 |     environment:
37 |       name: github-pages
38 |       url: ${{ steps.deployment.outputs.page_url }}
39 |     runs-on: ubuntu-latest
40 |     steps:
41 |       - name: Deploy to GitHub Pages
42 |         id: deployment
43 |         uses: actions/deploy-pages@v4
44 |         with:
45 |           artifact_name: "WDL Documentation"
46 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
1 | .DS_Store
2 | node_modules/
3 | 
4 | # Disable the Vitepress cache.
5 | .vitepress/cache/*
6 | 
7 | # Disable the Vitepress distribution folder.
8 | .vitepress/dist/*
9 | 


--------------------------------------------------------------------------------
/.vitepress/config.mts:
--------------------------------------------------------------------------------
  1 | import { defineConfig } from "vitepress";
  2 | import axios from "axios";
  3 | 
  4 | const url =
  5 |   "https://raw.githubusercontent.com/stjude-rust-labs/sprocket-vscode/refs/heads/main/syntaxes/wdl.tmGrammar.json";
  6 | 
  7 | /**
  8 |  * Gets the current version of the Sprocket TextMate grammar.
  9 |  * @returns the TextMate grammar as a JavaScript object
 10 |  */
 11 | async function getGrammar() {
 12 |   try {
 13 |     var response = await axios.get(url);
 14 |     return response.data;
 15 |   } catch (error) {
 16 |     console.error(`error occurred: ${error}`);
 17 |     throw error;
 18 |   }
 19 | }
 20 | 
 21 | export default defineConfig({
 22 |   title: "Workflow Description Language (WDL) Documentation",
 23 |   description:
 24 |     "Guides and reference materials for the Workflow Description Language (WDL).",
 25 |   appearance: "force-dark",
 26 |   base: "/",
 27 |   ignoreDeadLinks: ["./LICENSE"],
 28 |   head: [
 29 |     ["link", { rel: "icon", href: "/favicon.ico" }],
 30 |     ["link", { rel: "preconnect", href: "https://fonts.googleapis.com" }],
 31 |     [
 32 |       "link",
 33 |       { rel: "preconnect", href: "https://fonts.gstatic.com", crossorigin: "" },
 34 |     ],
 35 |     [
 36 |       "link",
 37 |       {
 38 |         href: "https://fonts.googleapis.com/css2?family=Martian+Mono:wght@100..800&family=Public+Sans:ital,wght@0,100..900;1,100..900&display=swap",
 39 |         rel: "stylesheet",
 40 |       },
 41 |     ],
 42 |   ],
 43 |   themeConfig: {
 44 |     /**
 45 |      * Logo and site title.
 46 |      */
 47 |     logo: {
 48 |       src: "/logo-only.svg",
 49 |       alt: "The Workflow Description Language (WDL) logo.",
 50 |     },
 51 |     siteTitle: "Documentation",
 52 | 
 53 |     /**
 54 |      * Navbar.
 55 |      */
 56 |     nav: [
 57 |       {
 58 |         text: "Specification",
 59 |         link: "https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md",
 60 |       },
 61 |     ],
 62 | 
 63 |     socialLinks: [
 64 |       {
 65 |         icon: "slack",
 66 |         link: "https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw",
 67 |       },
 68 |       { icon: "github", link: "https://github.com/openwdl/docs" },
 69 |     ],
 70 | 
 71 |     search: {
 72 |       provider: "local",
 73 |     },
 74 | 
 75 |     /**
 76 |      * Sidebar.
 77 |      */
 78 |     sidebar: [
 79 |       { text: "Overview", link: "/overview" },
 80 |       {
 81 |         text: "Getting Started",
 82 |         items: [
 83 |           { text: "Quickstart", link: "/getting-started/quickstart" },
 84 |           { text: "Ecosystem", link: "/getting-started/ecosystem" },
 85 |           { text: "Getting help", link: "/getting-started/getting-help" },
 86 |           { text: "Contributing", link: "/getting-started/contributing" },
 87 |         ],
 88 |       },
 89 |       {
 90 |         text: "Language Guide",
 91 |         items: [
 92 |           { text: "Variables", link: "/language-guide/variables.md" },
 93 |           { text: "Structs", link: "/language-guide/structs.md" },
 94 |           { text: "Tasks", link: "/language-guide/tasks.md" },
 95 |           { text: "Workflows", link: "/language-guide/workflows.md" },
 96 |           { text: "Imports", link: "/language-guide/imports.md" },
 97 |           { text: "Versions", link: "/language-guide/versions.md" },
 98 |         ],
 99 |       },
100 |       {
101 |         text: "Design Patterns",
102 |         items: [
103 |           {
104 |             text: "Linear chaining",
105 |             link: "/design-patterns/linear-chaining/index.md",
106 |           },
107 |           {
108 |             text: "Multiple I/O",
109 |             link: "/design-patterns/multiple-io/index.md",
110 |           },
111 |           {
112 |             text: "Branch and merge",
113 |             link: "/design-patterns/branch-and-merge/index.md",
114 |           },
115 |           {
116 |             text: "Task aliasing",
117 |             link: "/design-patterns/task-aliasing/index.md",
118 |           },
119 |           {
120 |             text: "Conditional statement",
121 |             link: "/design-patterns/conditional-statement/index.md",
122 |           },
123 |           {
124 |             text: "Scatter-gather",
125 |             link: "/design-patterns/scatter-gather/index.md",
126 |           },
127 |         ],
128 |       },
129 |       {
130 |         text: "Reference",
131 |         items: [
132 |           {
133 |             text: "Upgrade guide",
134 |             link: "/reference/upgrade-guide",
135 |           },
136 |           {
137 |             text: "Standard library",
138 |             items: [
139 |               {
140 |                 text: "Numeric functions",
141 |                 link: "/reference/stdlib/numeric",
142 |               },
143 |               {
144 |                 text: "String functions",
145 |                 link: "/reference/stdlib/string",
146 |               },
147 |               {
148 |                 text: "File functions",
149 |                 link: "/reference/stdlib/file",
150 |               },
151 |               {
152 |                 text: "String Array functions",
153 |                 link: "/reference/stdlib/string-array",
154 |               },
155 |             ],
156 |             collapsed: true,
157 |           },
158 |         ],
159 |       },
160 |       {
161 |         text: "Links",
162 |         items: [
163 |           {
164 |             text: "Cookbook",
165 |             link: "https://github.com/openwdl/cookbook",
166 |           },
167 |         ],
168 |       },
169 |     ],
170 |   },
171 |   markdown: {
172 |     theme: "github-dark",
173 |     shikiSetup: async function (highlighter) {
174 |       // Adds the WDL TextMate grammar from the `stjude-rust-labs/sprocket-vscode` repo
175 |       // to the Shiki highlighter.
176 |       await highlighter.loadLanguage(getGrammar());
177 |     },
178 |   },
179 | });
180 | 


--------------------------------------------------------------------------------
/.vitepress/theme/index.ts:
--------------------------------------------------------------------------------
 1 | // https://vitepress.dev/guide/custom-theme
 2 | import { h } from "vue";
 3 | import type { Theme } from "vitepress";
 4 | import DefaultTheme from "vitepress/theme";
 5 | import "./style.css";
 6 | 
 7 | export default {
 8 |   extends: DefaultTheme,
 9 |   Layout: () => {
10 |     return h(DefaultTheme.Layout, null, {
11 |       // https://vitepress.dev/guide/extending-default-theme#layout-slots
12 |     });
13 |   },
14 |   enhanceApp({ app, router, siteData }) {
15 |     // ...
16 |   },
17 | } satisfies Theme;
18 | 


--------------------------------------------------------------------------------
/.vitepress/theme/style.css:
--------------------------------------------------------------------------------
  1 | /**
  2 |  * Customize default theme styling by overriding CSS variables:
  3 |  * https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css
  4 |  */
  5 | 
  6 | /**
  7 |  * Colors
  8 |  *
  9 |  * Each colors have exact same color scale system with 3 levels of solid
 10 |  * colors with different brightness, and 1 soft color.
 11 |  *
 12 |  * - `XXX-1`: The most solid color used mainly for colored text. It must
 13 |  *   satisfy the contrast ratio against when used on top of `XXX-soft`.
 14 |  *
 15 |  * - `XXX-2`: The color used mainly for hover state of the button.
 16 |  *
 17 |  * - `XXX-3`: The color for solid background, such as bg color of the button.
 18 |  *   It must satisfy the contrast ratio with pure white (#ffffff) text on
 19 |  *   top of it.
 20 |  *
 21 |  * - `XXX-soft`: The color used for subtle background such as custom container
 22 |  *   or badges. It must satisfy the contrast ratio when putting `XXX-1` colors
 23 |  *   on top of it.
 24 |  *
 25 |  *   The soft color must be semi transparent alpha channel. This is crucial
 26 |  *   because it allows adding multiple "soft" colors on top of each other
 27 |  *   to create a accent, such as when having inline code block inside
 28 |  *   custom containers.
 29 |  *
 30 |  * - `default`: The color used purely for subtle indication without any
 31 |  *   special meanings attched to it such as bg color for menu hover state.
 32 |  *
 33 |  * - `brand`: Used for primary brand colors, such as link text, button with
 34 |  *   brand theme, etc.
 35 |  *
 36 |  * - `tip`: Used to indicate useful information. The default theme uses the
 37 |  *   brand color for this by default.
 38 |  *
 39 |  * - `warning`: Used to indicate warning to the users. Used in custom
 40 |  *   container, badges, etc.
 41 |  *
 42 |  * - `danger`: Used to show error, or dangerous message to the users. Used
 43 |  *   in custom container, badges, etc.
 44 |  * -------------------------------------------------------------------------- */
 45 | 
 46 | :root {
 47 |   --vp-c-default-1: var(--vp-c-gray-1);
 48 |   --vp-c-default-2: var(--vp-c-gray-2);
 49 |   --vp-c-default-3: var(--vp-c-gray-3);
 50 |   --vp-c-default-soft: var(--vp-c-gray-soft);
 51 | 
 52 |   --vp-c-black: #161619;
 53 | 
 54 |   --vp-c-brand-1: #00b4e1;
 55 |   --vp-c-brand-2: #0a96c3;
 56 |   --vp-c-brand-3: #006587;
 57 |   --vp-c-brand-soft: var(--vp-c-indigo-soft);
 58 | 
 59 |   --vp-c-text-1: #D6D6D6;
 60 | 
 61 |   --vp-c-tip-1: var(--vp-c-brand-1);
 62 |   --vp-c-tip-2: var(--vp-c-brand-2);
 63 |   --vp-c-tip-3: var(--vp-c-brand-3);
 64 |   --vp-c-tip-soft: var(--vp-c-brand-soft);
 65 | 
 66 |   --vp-c-warning-1: var(--vp-c-yellow-1);
 67 |   --vp-c-warning-2: var(--vp-c-yellow-2);
 68 |   --vp-c-warning-3: var(--vp-c-yellow-3);
 69 |   --vp-c-warning-soft: var(--vp-c-yellow-soft);
 70 | 
 71 |   --vp-c-danger-1: var(--vp-c-red-1);
 72 |   --vp-c-danger-2: var(--vp-c-red-2);
 73 |   --vp-c-danger-3: var(--vp-c-red-3);
 74 |   --vp-c-danger-soft: var(--vp-c-red-soft);
 75 | }
 76 | 
 77 | /**
 78 |  * Component: Fonts
 79 |  * -------------------------------------------------------------------------- */
 80 | 
 81 | :root {
 82 |   --vp-font-family-base: "Public Sans";
 83 |   --vp-font-family-mono: "Martian Mono";
 84 |   --vp-code-font-size: 12px;
 85 | 
 86 |   .text {
 87 |     font-size: 15px;
 88 |     line-height: 18px;
 89 |   }
 90 | 
 91 |   .VPFeatures p {
 92 |     font-size: 17px;
 93 |     line-height: 20px;
 94 |   }
 95 | 
 96 |   .VPSidebarItem h2 {
 97 |     margin-bottom: 4px;
 98 |   }
 99 | 
100 |   .content:not(code) {
101 |     font-size: 17px;
102 |     line-height: 26px !important;
103 |   }
104 | 
105 |   .details {
106 |     line-height: 26px !important;
107 |   }
108 | }
109 | 
110 | 
111 | /**
112 |  * Component: Sidebar
113 |  * -------------------------------------------------------------------------- */
114 | 
115 | :root {
116 |   --vp-layout-max-width: 1325px;
117 | }
118 | 
119 | .VPDoc:not(.has-sidebar) .container {
120 |   max-width: 100% !important;
121 | }
122 | 
123 | .VPDoc:not(.has-sidebar) .content {
124 |   max-width: 100% !important;
125 | }
126 | 
127 | .VPDoc.has-aside .content-container {
128 |   max-width: 100% !important;
129 | }
130 | 
131 | /**
132 |  * Component: Button
133 |  * -------------------------------------------------------------------------- */
134 | 
135 | :root {
136 |   --vp-button-brand-border: transparent;
137 |   --vp-button-brand-text: var(--vp-c-white);
138 |   --vp-button-brand-bg: var(--vp-c-brand-2);
139 |   --vp-button-brand-hover-border: transparent;
140 |   --vp-button-brand-hover-text: var(--vp-c-white);
141 |   --vp-button-brand-hover-bg: var(--vp-c-brand-1);
142 |   --vp-button-brand-active-border: transparent;
143 |   --vp-button-brand-active-text: var(--vp-c-white);
144 |   --vp-button-brand-active-bg: var(--vp-c-brand-3);
145 | }
146 | 
147 | /**
148 |  * Component: Home
149 |  * -------------------------------------------------------------------------- */
150 | 
151 | :root {
152 |   --vp-home-hero-name-color: transparent;
153 | 
154 |   --vp-home-hero-name-background: #ffffff;
155 | 
156 |   --vp-home-hero-image-background-image: linear-gradient(
157 |     -45deg,
158 |     #00b4e1 50%,
159 |     #47caff 50%
160 |   );
161 |   --vp-home-hero-image-filter: blur(44px);
162 | }
163 | 
164 | @media (min-width: 640px) {
165 |   :root {
166 |     --vp-home-hero-image-filter: blur(56px);
167 |   }
168 | }
169 | 
170 | @media (min-width: 960px) {
171 |   :root {
172 |     --vp-home-hero-image-filter: blur(68px);
173 |   }
174 | }
175 | 
176 | /**
177 |  * Component: Custom Block
178 |  * -------------------------------------------------------------------------- */
179 | 
180 | :root {
181 |   --vp-custom-block-tip-border: transparent;
182 |   --vp-custom-block-tip-text: var(--vp-c-text-1);
183 |   --vp-custom-block-tip-bg: var(--vp-c-brand-soft);
184 |   --vp-custom-block-tip-code-bg: var(--vp-c-brand-soft);
185 | }
186 | 
187 | /**
188 |  * Component: Algolia
189 |  * -------------------------------------------------------------------------- */
190 | 
191 | .DocSearch {
192 |   --docsearch-primary-color: var(--vp-c-brand-1) !important;
193 | }
194 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | BSD 3-Clause License
 2 | 
 3 | Copyright (c) 2022, OpenWDL
 4 | All rights reserved.
 5 | 
 6 | Redistribution and use in source and binary forms, with or without
 7 | modification, are permitted provided that the following conditions are met:
 8 | 
 9 | 1. Redistributions of source code must retain the above copyright notice, this
10 |    list of conditions and the following disclaimer.
11 | 
12 | 2. Redistributions in binary form must reproduce the above copyright notice,
13 |    this list of conditions and the following disclaimer in the documentation
14 |    and/or other materials provided with the distribution.
15 | 
16 | 3. Neither the name of the copyright holder nor the names of its
17 |    contributors may be used to endorse or promote products derived from
18 |    this software without specific prior written permission.
19 | 
20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | <div style="align: center">
 2 |   <img src=".github/assets/readme-header.svg">
 3 | </div>
 4 | 
 5 | <br />
 6 | 
 7 | This repository contains the official WDL community documentation. Enclosed you'll find
 8 | community-developed content, such as tutorials, guides, and language reference
 9 | materials, that appeal to old and new WDL users alike. Further, you'll find an
10 | up-to-date list of community tools and resources that you can leverage in your work.
11 | Feel free to [join Slack][join-slack] if you have any questions!
12 | 
13 | ## Quickstart 
14 | 
15 | You can use the following commands to get started working with the WDL community
16 | documentation. We recommend installing [`pnpm`](https://pnpm.io/installation), but `npm`
17 | will also work just fine.
18 | 
19 | ```bash
20 | # Install the project.
21 | pnpm install
22 | 
23 | # Run a development server.
24 | pnpm run docs:dev
25 | 
26 | # Create a production build in the `.vitepress/dist` folder.
27 | pnpm run docs:build
28 | ```
29 | 
30 | ### Contributing
31 | 
32 | WDL only advances through community contributions. While participating in discussions
33 | and submitting issues are great ways to be involved, help is also needed to implement
34 | changes to the specification. For more information on how you can contribute, please
35 | read the [Contributing] guide.
36 | 
37 | ### License
38 | 
39 | The WDL documentation is made available to you under the permissive [BSD 3-Clause
40 | License](./LICENSE).
41 | 
42 | © 2022-Present The OpenWDL Developers
43 | 
44 | [join-slack]:
45 |     https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw
46 | [Contributing]: https://github.com/openwdl/governance/blob/main/CONTRIBUTING.md
47 | 


--------------------------------------------------------------------------------
/design-patterns/branch-and-merge/header.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/openwdl/docs/b6bc4b502d9b10cf785a01d3cbfe8c31595694f0/design-patterns/branch-and-merge/header.png


--------------------------------------------------------------------------------
/design-patterns/branch-and-merge/index.md:
--------------------------------------------------------------------------------
  1 | # Branch and merge
  2 | 
  3 | The ability to connect inputs and outputs described in the [Linear
  4 | chaining](../linear-chaining/index.md) and [Multiple
  5 | I/O](../multiple-io/index.md) chapters can be further extended to direct a
  6 | task's outputs to separate computation paths and merge the results together.
  7 | This technique, known as **branching and merging**, is a common way to run
  8 | multiple steps of a broader analysis in parallel.
  9 | 
 10 | ![A diagram showing four tasks: `stepA`, `stepB`, `stepC`, and `stepD`. The first task
 11 | (`stepA`) accepts no inputs and produces a single output (`out`). The second task
 12 | (`stepB`) and third tasks (`stepC`) have a single input (`in`) that is connected to the
 13 | `out` output from `stepA`. Each of these tasks has an output named `out`. The fourth
 14 | task (`stepD`) has two input: (a) `in1`, which is connected to `out` from `stepB` and
 15 | (b) `in2`, which is connected to `out` from `stepC`. This step has one output called
 16 | `out`. This forms a structure where `stepA` is executed first, `stepB` and `stepC` are
 17 | executed in parallel (the branch), and `stepD` waits on the results of these two
 18 | computations before finally executing (the merge).](header.png)
 19 | 
 20 | This often takes a form similar to the following example.
 21 | 
 22 | ```wdl
 23 | # ... task definitions ...
 24 | 
 25 | workflow run {
 26 |   # Run the first task.
 27 |   call stepA {}
 28 | 
 29 |   # Run `stepB`, connecting the `in` input to `stepA`'s `out` output.
 30 |   call stepB { input: in = stepA.out }
 31 | 
 32 |   # Run `stepC`, connecting the `in` input to `stepA`'s `out` output.
 33 |   call stepC { input: in = stepA.out }
 34 | 
 35 |   # Run `stepD`, connecting the `in1` input to `stepB`'s `out` output
 36 |   # and the `in2` input to `stepC`'s `out` output.
 37 |   call stepC { input: in1 = stepB.out, in2 = stepC.out }
 38 | }
 39 | ```
 40 | 
 41 | ## Continuing our example
 42 | 
 43 | To build on the example started in [Multiple I/O](../multiple-io/index.md#an-example),
 44 | we'll extend this workflow to have a filtering step for single nucleotide polymorphisms
 45 | and indels separately. This introduces a branch in our computation graph where the
 46 | filtering steps can be run concurrently and merged back together after completion.
 47 | 
 48 | ```wdl
 49 | version 1.2
 50 | 
 51 | # (1) We write a task to split the VCF into multiple VCFs.
 52 | task split_vcf {
 53 |   input {
 54 |     File vcf
 55 |   }
 56 | 
 57 |   command <<<
 58 |     cp ~/Desktop/wdl/file.vcf.gz .
 59 | 
 60 |     picard SplitVcfs \
 61 |       I="~{vcf}" \
 62 |       SNP_OUTPUT="snp.vcf" \
 63 |       INDEL_OUTPUT="indel.vcf" \
 64 |       STRICT=false
 65 |     >>>
 66 | 
 67 |   output {
 68 |     File snp_vcf = "snp.vcf"
 69 |     File indel_vcf = "indel.vcf"
 70 |   }
 71 | }
 72 | 
 73 | # (2) We write a task to filter SNPs using our criteria.
 74 | task filter_snps {
 75 |   input {
 76 |     File vcf
 77 |   }
 78 | 
 79 |   command <<<
 80 |     gatk VariantFiltration \
 81 |       -V ~{vcf} \
 82 |       -O filtered.vcf \
 83 |       --filter-expression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" \
 84 |       --filter-name "snp_filter"
 85 |   >>>
 86 | 
 87 |   output {
 88 |     File filtered_vcf = "filtered.vcf"
 89 |   }
 90 | }
 91 | 
 92 | # (3) We write a task to filter INDELs using out criteria.
 93 | task filter_indels {
 94 |   input {
 95 |     File vcf
 96 |   }
 97 | 
 98 |   command <<<
 99 |     gatk VariantFiltration \
100 |       -V ~{vcf} \
101 |       -O filtered.vcf \
102 |       --filter-expression "QD < 2.0 || FS > 200.0 || ReadPosRankSum <-20.0" \
103 |       --filter-name "indel_filter"
104 |   >>>
105 | 
106 |   output {
107 |     File filtered_vcf = "filtered.vcf"
108 |   }
109 | }
110 | 
111 | # (4) We write a task to merge these two VCFs.
112 | task merge_vcfs {
113 |   input {
114 |     File snp_vcf
115 |     File indel_vcf
116 |   }
117 | 
118 |   command <<<
119 |     picard MergeVcfs \
120 |       I="~{snp_vcf}" \
121 |       I="~{indel_vcf}" \
122 |       O="combined.vcf"
123 |   >>>
124 | 
125 |   output {
126 |     File combined = "combined.vcf"
127 |   }
128 | }
129 | 
130 | # (5) We write a workflow that branches to the two filtering steps
131 | # and merges back in the `merge_vcfs` task.
132 | workflow run {
133 |   input {
134 |     File vcf
135 |   }
136 | 
137 |   call split_vcf { input: vcf }
138 | 
139 |   # (a) The branch happens here.
140 |   call filter_snps { input: vcf = split_vcf.snp_vcf }
141 |   call filter_indels { input: vcf = split_vcf.indel_vcf }
142 | 
143 |   # (b) The merge happens here.
144 |   call merge_vcfs { input:
145 |     snp_vcf = filter_snps.filtered_vcf,
146 |     indel_vcf = filter_snps.filtered_vcf,
147 |   }
148 | 
149 |   output {
150 |     File combined = merge_vcfs.combined
151 |   }
152 | }
153 | ```
154 | 


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 1 | # Conditional statement
 2 | 
 3 | It is often desirable to only execute some section of a computation graph only if a
 4 | particular condition holds. This could be as simple as a user input to the workflow
 5 | indicating the "mode A" should be run instead of "mode B", whether to scatter and gather
 6 | tasks rather than running a single multi-threaded task, or enabling an entire analysis
 7 | based on if some analytical check passes a QC threshold. In these cases, you'll want to
 8 | reach for **conditional statements** (also known as `if`/`else` statements).
 9 | 
10 | ![A diagram showing three tasks: `stepA`, `stepB`, and `stepC`. `stepA` is always
11 | executed, and a conditional boolean variable named `perform_further_work` is gating the
12 | execution of the two downstream tasks (`taskB` and `taskC`).](header.png)
13 | 
14 | This often takes a form similar to the following example.
15 | 
16 | ```wdl
17 | # ... task definitions ...
18 | 
19 | workflow run {
20 |   inputs {
21 |     Boolean perform_further_work = true
22 |   }
23 | 
24 |   # Run the first task.
25 |   call stepA {}
26 | 
27 |   # If the conditional is true, run `stepB` and `stepC`.
28 |   if (perform_further_work) {
29 |     call stepB { input: in = stepA.out }
30 |     call stepC { input: in = stepB.out }
31 |   }
32 | }
33 | ```
34 | 
35 | This can also take the form of evaluating outputs from prior workflow steps. For
36 | example, if you had a task `stepA` that contained a `Boolean is_sufficient_quality`
37 | output, you could do the following.
38 | 
39 | ```wdl
40 | # ... task definitions ...
41 | 
42 | workflow run {
43 |   # Run the first task.
44 |   call stepA {}
45 | 
46 |   # If `stepA` determined the sample is of sufficient quality,
47 |   # run `stepB` and `stepC`.
48 |   if (stepA.is_sufficient_quality) {
49 |     call stepB { input: in = stepA.out }
50 |     call stepC { input: in = stepB.out }
51 |   }
52 | }
53 | ```
54 | 


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 1 | # Linear chaining
 2 | 
 3 | The simplest way to chain tasks together in a workflow is a **linear chain**, whereby
 4 | the outputs of one tasks feeds into the input of the next task. The diagram below show
 5 | the linear chaining of three tasks in a row.
 6 | 
 7 | ![A diagram showing linear chaining of three tasks: `stepA`, `stepB`, and `stepC`. Each
 8 | task is laid out linearly in the order described. The first task (`stepA`) accepts no
 9 | inputs and produces a single output (`out`). The second task (`stepB`) has a single
10 | input (`in`) that is connected to the `out` output from `stepA` and has a single output
11 | (`out`). The third task (`stepC`) has a single input (`in`) that is connected to the
12 | `out` output from `stepB` and has no outputs. This forms a linear execution chain of
13 | these tasks.](header.png)
14 | 
15 | WDL allows this to be expressed simply, as the output of any task (declared in the
16 | `output` section of the task) may be used as an input to another task when it is called
17 | (via the `call` directive).
18 | 
19 | ```wdl
20 | # ... task definitions ...
21 | 
22 | workflow run {
23 |   # Run the first task.
24 |   call stepA {}
25 | 
26 |   # Run `stepB`, connecting the `in` input to `stepA`'s `out` output.
27 |   call stepB { input: in = stepA.out }
28 | 
29 |   # Run `stepC`, connecting the `in` input to `stepB`'s `out` output.
30 |   call stepC { input: in = stepB.out }
31 | }
32 | ```
33 | 
34 | This works because each task creates a _scope_ of the same name as the task that
35 | contains that tasks outputs. Similarly, when using a `call` directive, you can set
36 | values of the inputs within that task's scope.
37 | 
38 | ## A full example
39 | 
40 | For a more complete picture, here is a workflow that actually computes π by getting the
41 | constant from Python.
42 | 
43 | ```wdl
44 | version 1.2
45 | 
46 | # (1) We write a task to calculate π.
47 | task calculate_pi {
48 |   command <<<
49 |     python3 -c "import math; print(math.pi)"
50 |   >>>
51 | 
52 |   output {
53 |     # (a) π is output as an _output_ of this task here.
54 |     # It's read from standard input and parsed as a `Float`.
55 |     Float pi = read_float(stdout())
56 |   }
57 | }
58 | 
59 | # (2) We write a task that takes in the output from the
60 | # previous task and uses it to compute the area of a circle.
61 | task calculate_circle_area {
62 |   input {
63 |     # (a) π is taken as an input here.
64 |     Float pi
65 |     Float radius = 5.0
66 |   }
67 | 
68 |   command <<<
69 |     bc -l <<< "2 * ~{pi} * ~{radius}"
70 |   >>>
71 | 
72 |   output {
73 |     Float area = read_float(stdout())
74 |   }
75 | }
76 | 
77 | # (3) We write a workflow that linearly chains the two tasks
78 | # by connecting the output of the first task to the input of
79 | # the second task.
80 | workflow hello {
81 |   # (a) π is calculated in this step.
82 |   call calculate_pi
83 | 
84 |   # (b) the output from the `calculate_pi` step is passed to
85 |   # the input of the `calculate_circle_area` input here.
86 |   call calculate_circle_area { input: pi = calculate_pi.pi }
87 | 
88 |   output {
89 |     Float area = calculate_circle_area.area
90 |   }
91 | }
92 | 
93 | # Now, π will first be calculated by calling `calculate_pi`
94 | # and, once that has completed, `calculate_circle_area` will
95 | # be called using the calculated constant.
96 | ```
97 | 


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  1 | # Multiple I/O
  2 | 
  3 | Tasks don't only have to have a single input and output: they can produce accept
  4 | **multiple inputs**, produce **multiple outputs**, and workflows can easily specify
  5 | which inputs and outputs need to be connected together. For example, take the consider
  6 | the following example.
  7 | 
  8 | ![A diagram showing linear chaining of three tasks: `stepA`, `stepB`, and `stepC`. The
  9 | first task (`stepA`) accepts no inputs and produces a single output (`out`). The second
 10 | task (`stepB`) has a single input (`in`) that is connected to the `out` output from
 11 | `stepA` and has two outputs: `out1` and `out2`. The third task (`stepC`) has two inputs
 12 | (`in1` and `in2`) that are connected to `out1` and `out2` from `stepB` respectively.
 13 | `stepC` has no outputs. This forms a linear chain for these tasks, except that multiple
 14 | inputs in `stepC` are connected to multiple outputs in `stepB` to illustrate the
 15 | multiple inputs and multiple outputs concept.](header.png)
 16 | 
 17 | Notice that the two outputs from `stepB` have distinctive types and names. Further, the
 18 | two inputs in `stepC` has distinctive types and names as well. Because of this, you can
 19 | easily direct a workflow to connect the outputs in `stepB` to their respective inputs in
 20 | `stepC`.
 21 | 
 22 | ```wdl
 23 | # ... task definitions ...
 24 | 
 25 | workflow run {
 26 |   # Run `stepA`.
 27 |   call stepA {}
 28 | 
 29 |   # Run `stepB`, connecting the `in` input to `stepA`'s `out` output.
 30 |   call stepB { input: in = stepA.out }
 31 | 
 32 |   # Run `stepC`, connecting the `in1` and `in2` inputs to `stepB`'s
 33 |   # `out1` and `out2` outputs, respectively.
 34 |   call stepC { input:
 35 |     in1 = stepB.out1,
 36 |     in2 = stepB.out2
 37 |   }
 38 | }
 39 | ```
 40 | 
 41 | Again, because each task creates a scope containing each output, the correct inputs and
 42 | outputs can be connected together, and names will not conflict.
 43 | 
 44 | ## An example
 45 | 
 46 | To illustrate this concept, here is an example workflow that uses
 47 | [Picard](https://broadinstitute.github.io/picard/) to split a VCF into (a) a VCF
 48 | containing only single nucleotide variants and (b) a VCF containing only
 49 | insertions/deletions, followed by merging them back together.
 50 | 
 51 | ```wdl
 52 | version 1.2
 53 | 
 54 | # (1) We write a task to split the VCF into multiple VCFs.
 55 | task split_vcf {
 56 |   input {
 57 |     # (a) The task takes in a single input VCF.
 58 |     File vcf
 59 |   }
 60 | 
 61 |   command <<<
 62 |     java -jar picard.jar SplitVcfs \
 63 |       I="~{vcf}" \
 64 |       SNP_OUTPUT="snp.vcf" \
 65 |       INDEL_OUTPUT="indel.vcf" \
 66 |       STRICT=false
 67 |   >>>
 68 | 
 69 |   output {
 70 |     # (b) The task produces two output VCFs.
 71 |     File snp_vcf = "snp.vcf"
 72 |     File indel_vcf = "indel.vcf"
 73 |   }
 74 | }
 75 | 
 76 | # (2) We write a task to merge these two VCFs.
 77 | task merge_vcfs {
 78 |   input {
 79 |     # (a) Two input VCFs are accepted.
 80 |     File snp_vcf
 81 |     File indel_vcf
 82 |   }
 83 | 
 84 |   command <<<
 85 |     java -jar picard.jar MergeVcfs \
 86 |       I="~{snp_vcf}" \
 87 |       I="~{indel_vcf}" \
 88 |       O="combined.vcf"
 89 |   >>>
 90 | 
 91 |   output {
 92 |     # (b) One output VCF is produced.
 93 |     File combined = "combined.vcf"
 94 |   }
 95 | }
 96 | 
 97 | # (3) We write a workflow that connects the multiple outputs
 98 | # from the `split_vcf` task into the multiple inputs from the
 99 | # `merge_vcfs` task.
100 | workflow run {
101 |   input {
102 |     File vcf
103 |   }
104 | 
105 |   call split_vcf { input: vcf }
106 | 
107 |   # (a) The outputs are connected to the inputs here.
108 |   call merge_vcfs { input:
109 |     snp_vcf = split_vcf.snp_vcf,
110 |     indel_vcf = split_vcf.indel_vcf,
111 |   }
112 | 
113 |   output {
114 |     File combined = merge_vcfs.combined
115 |   }
116 | }
117 | ```
118 | 


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 1 | # Scatter-gather
 2 | 
 3 | Scatter-gather is a paradigm of parallel computing whereby a computation is split into
 4 | smaller, independent pieces, those pieces "scattered" across multiple, parallel
 5 | executions, and the results each execution is "gathered" into a single result. This is
 6 | incredibly useful when attempting to optimize the speed of computations that don't
 7 | depend on one another. Some examples of this design pattern in practice include (a)
 8 | scattering of a complex analysis for a single sample across multiple, independent
 9 | chromosomes and merging the results together or (b) scattering the generation of
10 | independent [gVCFs] from multiple samples, followed by a gathering [joint genotyping
11 | step] employed by the GATK.
12 | 
13 | ![A diagram showing two steps: `stepA` and `stepB`. Multiple instances of `stepA` are
14 | called—one instance for each input file. Each of these produces an output (`out`).
15 | `stepB` is then called once accepting all of these `out` from each `stepA` call and
16 | combining the results. This, in essence, is the power of the scatter-gather
17 | paradigm.](header.png)
18 | 
19 | This often takes a form similar to the following example.
20 | 
21 | ```wdl
22 | # ... task definitions ...
23 | 
24 | workflow run {
25 |   inputs {
26 |     Array[File] files
27 |   }
28 | 
29 |   # Perform `stepA` for each of the inputs in parallel (scatter).
30 |   scatter(file in files) {
31 |     call stepA { input: in = file }
32 |   }
33 | 
34 |   # Collect the results from the scatter (gather).
35 |   #
36 |   # Note that the outputs from `stepA` are automatically coerced
37 |   # into an `Array` that you can pass in elsewhere.
38 |   call stepB { input: files = stepA.out }
39 | }
40 | ```
41 | 
42 | [gVCFs]:
43 |     https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format
44 | [joint genotyping step]:
45 |     https://gatk.broadinstitute.org/hc/en-us/articles/360037057852-GenotypeGVCFs
46 | 


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 1 | # Task aliasing
 2 | 
 3 | Occasionally, you will need to call the same task multiple times within the same
 4 | workflow. For example, you might need to run the same variant caller between two samples
 5 | to determine the variants that are unique to one. Another interesting use case might be
 6 | to run the same variant caller on the same sample with different parameters to examine
 7 | the differences. In these cases, you'll want to reach for **task aliasing** to ensure
 8 | that the names for each `call` remain unique.
 9 | 
10 | ![A diagram showing three steps: `stepA`, `stepB`, and `stepC`. `stepA` is run twice
11 | with aliases `first` and `second`: both of these instances take one input from
12 | (`sampleA` and `sampleB` respectively) and produce a single output (`out`). `taskB`
13 | takes one input (`in`) that is connected to `out` from `first`. `taskC`
14 | takes one input (`in`) that is connected to `out` from `second`. Both `taskB` and
15 | `taskC` produce a single output (`out`). In this way, the utility of aliasing multiple
16 | `call`s of the same task is demonstrated.](header.png)
17 | 
18 | This often takes a form similar to the following example.
19 | 
20 | ```wdl
21 | # ... task definitions ...
22 | 
23 | workflow run {
24 |     # `taskA` is run twice—this is enabled using task aliasing.
25 |     call stepA as first {}
26 |     call stepA as second {}
27 | 
28 |     # `taskB` takes in the output from the `first` task.
29 |     call stepB { input: in = first.out }
30 | 
31 |     # `taskC` takes in the output from the `second` task.
32 |     call stepC { input: in = second.out }
33 | }
34 | ```
35 | 
36 | [gVCFs]:
37 |     https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format
38 | [joint genotyping step]:
39 |     https://gatk.broadinstitute.org/hc/en-us/articles/360037057852-GenotypeGVCFs
40 | 


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 1 | # Contributing
 2 | 
 3 | WDL is a community project and, thus, depends on _your_ contributions to make sure it
 4 | continues to thrive. Contributions can come in various forms, including
 5 | 
 6 | - filing issues when you run into problems on GitHub,
 7 | - participating as part of language design discussions (via the [RFC process]),
 8 | - contributing language or code changes via [pull requests], and
 9 | - helping answer questions on [Slack][slack-invite].
10 | 
11 | Please browse the [OpenWDL organization] to learn about the different parts of the
12 | project and get an idea of how you could contribute. Keep in mind that contributions to
13 | WDL must be contributed according to the `CONTRIBUTING.md` ([link][contributing-md])
14 | document.
15 | 
16 | ### Suggested first steps
17 | 
18 | While all of these projects are important, consider starting with the [specification]
19 | and [documentation] repositories. In particular keeping the documentation up to date is
20 | important—things like typo fixes, updates to existing content, suggestions for new
21 | documentation, and keeping the list of resources in the [Ecosystem](./ecosystem.md) page
22 | is incredibly helpful!
23 | 
24 | [documentation]: https://github.com/openwdl/docs/
25 | [OpenWDL organization]: https://github.com/openwdl/
26 | [pull requests]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request
27 | [RFC process]: https://github.com/openwdl/wdl/blob/wdl-1.2/RFC.md
28 | [slack-invite]: https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw
29 | [specification]: https://github.com/openwdl/wdl/
30 | [contributing-md]: https://github.com/openwdl/wdl/blob/wdl-1.2/CONTRIBUTING.md
31 | 


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  1 | # Ecosystem
  2 | 
  3 | WDL has a rich, distributed ecosystem of interconnected developer tools and execution
  4 | engines to ensure (a) users can quickly write high-quality, idiomatic workflows, and (b)
  5 | scaling the execution of those workflows within any computation environment is a breeze.
  6 | 
  7 | ::: tip
  8 | 
  9 | The WDL ecosystem is rapidly evolving, and, while we're always looking to expand
 10 | the list of known ecosystem tools, sometimes tools get missed. If you know of a tool
 11 | that needs to be listed here but isn't, we encourage you to [create a pull request] and
 12 | let us know!
 13 | 
 14 | :::
 15 | 
 16 | ## Execution Engines
 17 | 
 18 | The following list contains the known execution engines listed alphabetically.
 19 | 
 20 | <table>
 21 |   <tr>
 22 |     <th>Engine</th>
 23 |     <th>Local</th>
 24 |     <th>HPC</th>
 25 |     <th>Cloud</th>
 26 |   </tr>
 27 |   <tr>
 28 |     <td>
 29 |     <a href="https://docs.aws.amazon.com/omics/latest/dev/what-is-healthomics.html">
 30 |       AWS HealthOmics
 31 |     </a>
 32 |     <br />
 33 |     Hosted Platform <br />
 34 |     <i>Support WDL v1.1</i>
 35 |     </td>
 36 |     <td>
 37 |     <center>
 38 |       <input type="checkbox" disabled>
 39 |     </center>
 40 |     </td>
 41 |     <td>
 42 |       <input type="checkbox" disabled> Slurm <br />
 43 |       <input type="checkbox" disabled> IBM LSF
 44 |     </td>
 45 |     <td>
 46 |       <input type="checkbox" checked disabled> Amazon AWS <br />
 47 |       <input type="checkbox" disabled> Microsoft Azure <br />
 48 |       <input type="checkbox" disabled> Google Cloud
 49 |     </td>
 50 |   </tr>
 51 |   <tr>
 52 |     <td>
 53 |       <a href="https://github.com/broadinstitute/cromwell">
 54 |         Cromwell
 55 |       </a>
 56 |       <br />
 57 |     Binary/Executable <br />
 58 |     <i>Support WDL v1.0</i>
 59 |     </td>
 60 |     <td>
 61 |     <center>
 62 |       <input type="checkbox" checked disabled>
 63 |     </center>
 64 |     </td>
 65 |     <td>
 66 |       <input type="checkbox" checked disabled> Slurm <br />
 67 |       <input type="checkbox" checked disabled> IBM LSF
 68 |     </td>
 69 |     <td>
 70 |       <input type="checkbox" checked disabled> Amazon AWS <br />
 71 |       <input type="checkbox" checked disabled> Microsoft Azure <br />
 72 |       <input type="checkbox" checked disabled> Google Cloud
 73 |     </td>
 74 |   </tr>
 75 |   <tr>
 76 |     <td>
 77 |       <a href="https://github.com/dnanexus/dxCompiler">
 78 |         dxCompiler
 79 |       </a>
 80 |       <br />
 81 |     Binary/Executable <br />
 82 |     <i>Support WDL v1.1 and v2.0</i>
 83 |     </td>
 84 |     <td>
 85 |     <center>
 86 |       <input type="checkbox" disabled>
 87 |     </center>
 88 |     </td>
 89 |     <td>
 90 |       <input type="checkbox" disabled> Slurm <br />
 91 |       <input type="checkbox" disabled> IBM LSF
 92 |     </td>
 93 |     <td>
 94 |       <input type="checkbox" checked disabled> Amazon AWS* <br />
 95 |       <input type="checkbox" checked disabled> Microsoft Azure* <br />
 96 |       <input type="checkbox" disabled> Google Cloud <br /> <br />
 97 |       <i>* via DNAnexus</i>
 98 |     </td>
 99 |   </tr>
100 |   <tr>
101 |     <td>
102 |       <a href="https://github.com/chanzuckerberg/miniwdl">
103 |         miniwdl
104 |       </a>
105 |       <br />
106 |     Binary/Executable <br />
107 |     <i>Support WDL v1.1</i>
108 |     </td>
109 |     <td>
110 |     <center>
111 |       <input type="checkbox" checked disabled>
112 |     </center>
113 |     </td>
114 |     <td>
115 |       <input type="checkbox" checked disabled>
116 |         Slurm (<a href="https://github.com/miniwdl-ext/miniwdl-slurm">plugin</a>) <br />
117 |       <input type="checkbox" checked disabled>
118 |         IBM LSF (<a href="https://github.com/adthrasher/miniwdl-lsf">plugin</a>)
119 |     </td>
120 |     <td>
121 |       <input type="checkbox" checked disabled>
122 |         Amazon AWS (<a href="https://github.com/miniwdl-ext/miniwdl-aws">plugin</a>) <br />
123 |       <input type="checkbox" disabled> Microsoft Azure <br />
124 |       <input type="checkbox" disabled> Google Cloud
125 |     </td>
126 |   </tr>
127 |   <tr>
128 |     <td>
129 |       <a href="https://terra.bio/">
130 |         Terra
131 |       </a>
132 |       <br />
133 |     Hosted Platform <br />
134 |     <i>Support WDL v1.0</i>
135 |     </td>
136 |     <td>
137 |     <center>
138 |       <input type="checkbox" disabled>
139 |     </center>
140 |     </td>
141 |     <td>
142 |       <input type="checkbox" disabled> Slurm <br />
143 |       <input type="checkbox" disabled> IBM LSF
144 |     </td>
145 |     <td>
146 |       <input type="checkbox" disabled> Amazon AWS <br />
147 |       <input type="checkbox" checked disabled> Microsoft Azure <br />
148 |       <input type="checkbox" checked disabled> Google Cloud
149 |     </td>
150 |   </tr>
151 |    <tr>
152 |     <td>
153 |       <a href="https://toil.ucsc-cgl.org">
154 |         Toil
155 |       </a>
156 |       <br />
157 |     Binary/Executable <br />
158 |     <i>Support WDL v1.1</i>
159 |     </td>
160 |     <td>
161 |     <center>
162 |       <input type="checkbox" disabled>
163 |     </center>
164 |     </td>
165 |     <td>
166 |       <input type="checkbox" checked disabled> Slurm <br />
167 |       <input type="checkbox" checked disabled> IBM LSF
168 |     </td>
169 |     <td>
170 |       <input type="checkbox" checked disabled> Amazon AWS <br />
171 |       <input type="checkbox" disabled> Microsoft Azure <br />
172 |       <input type="checkbox" checked disabled> Google Cloud
173 |     </td>
174 |   </tr>
175 | </table>
176 | 
177 | 
178 | ## IDE Support
179 | 
180 | Extensions and other IDE support tools listed sorted by the editor.
181 | 
182 | | Name                                    | Editor             | Supports                                                                           |
183 | | :-------------------------------------- | :----------------- | :--------------------------------------------------------------------------------- |
184 | | [Sprocket][sprocket] (LSP)              | Editors with LSP   | Formatting, linting, snippets, syntax highlighting, and validation.                |
185 | | [wdl-mode]                              | Emacs              | Syntax highlighting.                                                               |
186 | | [poly-wdl]                              | Emacs              | Integration with [polymode].                                                       |
187 | | [Winstanly WDL]                         | JetBrains          | Linting and syntax highlighting.                                                   |
188 | | [wdl-sublime]                           | Sublime Text       | Syntax                                                               highlighting. |
189 | | [wdl-vim]                               | Vim                | Syntax highlighting.                                                               |
190 | | [Sprocket][sprocket-vscode] (extension) | Visual Studio Code | Formatting, linting, snippets, syntax highlighting, and validation.                |
191 | | [Syntax Highlighter]                    | Visual Studio Code | Syntax highlighting.                                                               |
192 | 
193 | ## Development Tools
194 | 
195 | The following are tools to enhance the experience of working with WDL sorted by
196 | the category.
197 | 
198 | | Name              | Category                 | Description                                               |
199 | | :---------------- | :----------------------- | :-------------------------------------------------------- |
200 | | [wdl-tests]       | Conformance testing      | Conformance tests for WDL execution engines.              |
201 | | [wdl-aid]         | Documentation generation | _"Automatic input generation for WDL worflows."_          |
202 | | [pytest-workflow] | Testing                  | Testing framework for workflow languages (including WDL). |
203 | | [wdldoc]          | Documentation generation | _"Create WDL documentation using Markdown."_              |
204 | | [wdl-packager]    | Package management       | _"Package a WDL and imports into a zip file."_            |
205 | | [pytest-wdl]      | Testing                  | _"WDL plugin for pytest."_                                |
206 | 
207 | ## Community Workflows
208 | 
209 | The following is an incomplete list of large WDL workflow repositories sorted by name.
210 | 
211 | | Name                                                            |  Description                                                                                                                                                                                                 |
212 | | :-------------------------------------------------------------- |  :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
213 | | [BioWDL] <br /> _LUMC_                                          |  _"Bioinformatics workflows and tasks, written in WDL."_ BioWDL is a large GitHub organization that contains the WDL workflows developed at LUMC ([link](https://lumc.nl)).                                  |
214 | | [Chan Zuckerberg] <br /> _Chan Zuckerberg Initiative_           | Official repository for the WDL workflows developed at the Chan Zuckerberg Initiative for the CZID platform ([link](https://czid.org)).                                                                     |
215 | | [Dockstore] <br /> _Multiple_                                   | Dockstore describes itself as "an app store for bioinformatics"—it's an open source platform for sharing analytical tools and workflows. WDL is one of the supported languages.                             |
216 | | [ENCODE] <br /> _ENCODE Consortium_                             | Official repository of the ENCODE Data Coordinating Center's Uniform Processing Pipelines. These pipelines are designed to "create high-quality, consistent, and reproducible data" for the ENCODE project. |
217 | | [GATK] <br /> _Broad Institute_                                 | Official GATK best practices workflows developed at and published by the Broad Institute's Data Sciences Platform.                                                                                          |
218 | | [PacBio] <br /> _Pacific Biosciences_                           | Official repository for the best practices workflows for PacBio data.                                                                                                                                       |
219 | | [St. Jude Cloud] <br /> _St. Jude Children's Research Hospital_ | Official repository for data processing pipelines used on St. Jude Cloud ([link](https://platform.stjude.cloud)).                                                                                           |
220 | | [Thiagen] <br /> _Theiagen Genomics_                            | Official repository of Thiagen's WDL workflows.                                                                                                                                                             |
221 | | [WARP] <br /> _Broad Institute_                                 | WARP stands for "WDL Research Analysis Pipelines" and contains cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform.                                    |
222 | | [WILDS] <br /> _Fred Hutch_                                     | Official repositories of the Workflows for Integration of Large Data and Software (WILDS) developed at the Fred Hutch Data Science Lab.                                                                     |
223 | 
224 | [create a pull request]: https://github.com/openwdl/docs/pulls
225 | [BioWDL]: https://github.com/biowdl
226 | [Chan Zuckerberg]: https://github.com/chanzuckerberg/czid-workflows
227 | [Dockstore]:
228 |     https://dockstore.org/search?descriptorType=WDL&entryType=workflows&searchMode=files
229 | [ENCODE]: https://www.encodeproject.org/pages/pipelines
230 | [GATK]: https://github.com/gatk-workflows/
231 | [PacBio]: https://github.com/orgs/PacificBiosciences/repositories?q=lang%3Awdl&type=all
232 | [poly-wdl]: https://github.com/jmonlong/poly-wdl
233 | [polymode]: https://github.com/polymode/polymode
234 | [pytest-wdl]: https://github.com/EliLillyCo/pytest-wdl
235 | [pytest-workflow]: https://github.com/LUMC/pytest-workflow
236 | [sprocket-vscode]:
237 |     https://marketplace.visualstudio.com/items?itemName=stjude-rust-labs.sprocket-vscode
238 | [sprocket]: https://github.com/stjude-rust-labs/sprocket
239 | [St. Jude Cloud]: https://github.com/stjudecloud/workflows
240 | [Syntax Highlighter]:
241 |     https://marketplace.visualstudio.com/items?itemName=broadinstitute.wdl
242 | [Thiagen]: https://github.com/theiagen/public_health_bioinformatics
243 | [WARP]: https://broadinstitute.github.io/warp/docs/get-started/
244 | [wdl-aid]: https://github.com/biowdl/wdl-aid
245 | [wdl-mode]: https://github.com/zhanxw/wdl-mode
246 | [wdl-packager]: https://github.com/biowdl/wdl-packager
247 | [wdl-sublime]: https://github.com/broadinstitutewdl-sublime/
248 | [wdl-tests]: https://github.com/openwdl/wdl-tests
249 | [wdl-vim]: https://github.com/broadinstitute/vim-wdl
250 | [wdldoc]: https://github.com/stjudecloud/wdldoc
251 | [WILDS]: https://github.com/orgs/getwilds/repositories?q=lang%3Awdl&type=all
252 | [Winstanly WDL]: https://plugins.jetbrains.com/plugin/8154-winstanley-wdl
253 | 


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/getting-started/getting-help.md:
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 1 | # Getting Help
 2 | 
 3 | The WDL community has a wide range of resources to help you when you need a helping
 4 | hand.
 5 | 
 6 | ### Questions
 7 | 
 8 | As you're learning WDL, you're bound to have questions. We suggest the following
 9 | mechanisms for getting the answers you need.
10 | 
11 | - Search the [discussions](https://github.com/openwdl/wdl/discussions) to see if your
12 |   question has been asked already; if it hasn't been asked, feel free start a new
13 |   discussion! If it's been asked but not yet answered, upvote the topic (if it's been
14 |   some time, also feel free to chime in on the thread)!
15 | - You may also join the community [Slack][slack-invite] and ask in the `#support`
16 |   channel. We highly prefer that you come to the Slack channel with an issue that you
17 |   can link us to, as responding to your issue helps us _more permanently_ answer the
18 |   question for future askers.
19 | 
20 | ### Bugs and new features
21 | 
22 | - Search the [issues](https://github.com/openwdl/wdl/issues) to see if someone's already
23 |   reported the issue. If your issue has _not_ already been reported, feel free to create
24 |   a new one!
25 |   - In particular, for feature requests, you are encouraged to start a discussion first
26 |     at one of the places in the section above to get community buy-in before proceeding.
27 | - If you'd like to provide a fix/implementation for an issue, please read about
28 |   [contributing][contributing-md] before submitting a [pull
29 |   request](https://github.com/openwdl/wdl/pulls).
30 | 
31 | ### Community Resources
32 | 
33 | Last, we have a number of official resources to make sure you have materials to learn
34 | from: be sure to check them out!
35 | 
36 | - The [official WDL documentation] (this site) is a great place to learn how to read and
37 |   write WDL. All of the basic information you need to get started should be here! how to
38 |   read and write WDL WDL.
39 | - If you're more of a guided learner, the [Learn WDL guide] walks you step-by-step
40 |   through the basics writing and running WDL—it even has an accompanying YouTube video!
41 | - The [official WDL template repository] is a starter template for a best practice WDL workflow
42 |   repository.
43 | - Last, the [WDL specification] exhaustively documents the WDL standard.
44 | 
45 | [contributing-md]: https://github.com/openwdl/wdl/blob/wdl-1.2/CONTRIBUTING.md
46 | [Learn WDL guide]: https://github.com/openwdl/learn-wdl
47 | [official WDL documentation]: https://github.com/openwdl/docs
48 | [official WDL template repository]: https://github.com/openwdl/workflow-template-wdl
49 | [slack-invite]: https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw
50 | [WDL specification]: https://github.com/openwdl/wdl
51 | 


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/getting-started/quickstart.md:
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  1 | # Quickstart
  2 | 
  3 | Welcome to the WDL quickstart guide 🚀! This brief guide gives an overview of all the
  4 | important bits of the WDL language to ensure you become an expert in writing your own
  5 | tasks and workflows. Before diving into an example, let's take a closer look at the
  6 | major concepts within the language.
  7 | 
  8 | ### Tasks
  9 | 
 10 | **Tasks** are the atomic units of computation within WDL. Tasks are comprised of a set
 11 | of inputs (defined within the `input` section), a set of outputs (defined within the
 12 | `output` section), and a command (defined within the `command` section), which is simply
 13 | a Bash script to execute. Tasks also support defining _requirements_ (defined within the
 14 | `requirements` section) which dictate certain aspects of the task runtime environment.
 15 | Importantly, tasks are executed within a [container][container-explanation] to ensure
 16 | portability across different execution environments (e.g., your local computer, an HPC,
 17 | or the cloud).
 18 | 
 19 | ### Workflows
 20 | 
 21 | **Workflows** string together tasks via their inputs and outputs into a larger
 22 | computation graph that can be executed. Workflows are arranged similarly to
 23 | tasks except that (a) they don't have a `command` or `requirements` section and
 24 | (b) they make available more control flow facilities that aren't relevant within
 25 | a task context. For example, the workflow below uses both _conditional
 26 | execution_ (the `if` statement) and a _scatter-gather_ (the `scatter` keyword
 27 | and `messages` output). Notably, workflows can also define inputs and outputs,
 28 | and these generally serve as the global inputs and outputs for the execution of
 29 | a workflow.
 30 | 
 31 | ### Inputs and Outputs
 32 | 
 33 | JSON is used for specifying both inputs to and outputs from a workflow. In the code
 34 | block below the workflow, you can see the inputs that are specified for the top-level
 35 | `name` parameter. You can also optionally provide a value for the `is_pirate`
 36 | parameter. Further, the output of the workflow is communicated back to you via JSON.
 37 | Executing workflows typically involves preparing the needed JSON files and reading the
 38 | outputs within the JSON returned from your execution engine.
 39 | 
 40 | ### An example
 41 | 
 42 | For example, assume you wanted to write a task that greets someone, as defined in the
 43 | `name` input, in multiple different languages. If that individual is a pirate, you might
 44 | even wish to greet them conditionally with `Ahoy`! WDL allows you to express this in a
 45 | straightforward manner by (a) constructing the atomic computation you'd like to achieve
 46 | using a `task` and (b) running that task for each of your greetings using a `workflow`.
 47 | 
 48 | ```wdl
 49 | version 1.2
 50 | 
 51 | task say_hello {
 52 |     input {
 53 |         String greeting
 54 |         String name
 55 |     }
 56 | 
 57 |     command <<<
 58 |         echo "~{greeting}, ~{name}!"
 59 |     >>>
 60 | 
 61 |     output {
 62 |         String message = read_string(stdout())
 63 |     }
 64 | 
 65 |     requirements {
 66 |         container: "ubuntu:latest"
 67 |     }
 68 | }
 69 | 
 70 | workflow main {
 71 |     input {
 72 |         String name
 73 |         Boolean is_pirate = false
 74 |     }
 75 | 
 76 |     Array[String] greetings = select_all([
 77 |         "Hello",
 78 |         "Hallo",
 79 |         "Hej",
 80 |         (
 81 |             if is_pirate
 82 |             then "Ahoy"
 83 |             else None
 84 |         ),
 85 |     ])
 86 | 
 87 |     scatter (greeting in greetings) {
 88 |         call say_hello {
 89 |             greeting,
 90 |             name,
 91 |         }
 92 |     }
 93 | 
 94 |     output {
 95 |         Array[String] messages = say_hello.message
 96 |     }
 97 | }
 98 | 
 99 | ```
100 | 
101 | #### Running the example
102 | 
103 | If you were to run the example above with these inputs,
104 | 
105 | ```json
106 | {
107 |   "main.name": "world",
108 |   // "main.is_pirate": true,
109 | }
110 | ```
111 | 
112 | the output of the above workflow would be the following.
113 | 
114 | ```json
115 | {
116 |   "messages": [
117 |     "Hello, world!",
118 |     "Hallo, world!",
119 |     "Hej, world!",
120 |     // "Ahoy, world!" is included is `is_pirate` is set to `true` above.
121 |   ]
122 | }
123 | ```
124 | 
125 | ### Conclusion
126 | 
127 | This workflow, though simple, demonstrates the how WDL accomplishes its main values:
128 | namely, its _human-readable/writable_ style and its _straightforward but powerful_
129 | control flow abstractions. You can learn more about the values of the WDL language on
130 | the [Overview](../overview.md#values) page.
131 | 
132 | [container-explanation]:
133 |     https://azure.microsoft.com/en-us/resources/cloud-computing-dictionary/what-is-a-container/
134 | 


--------------------------------------------------------------------------------
/index.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | # https://vitepress.dev/reference/default-theme-home-page
 3 | layout: home
 4 | 
 5 | hero:
 6 |   name: "Workflow Description Language Docs"
 7 |   tagline: Guides and reference materials for the Workflow Description Language (WDL).
 8 |   image: "hero.svg"
 9 |   actions:
10 |     - theme: brand
11 |       text: Get Started 🎉
12 |       link: /overview
13 |     - theme: alt
14 |       text: Join Slack 👋
15 |       link: https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw
16 | 
17 | features:
18 |   - icon: 🔎️
19 |     title: Human-readable and -writable
20 |     details: >
21 |       Designed to be written and understood by software engineers, domain experts,
22 |       and platform operators.
23 |   - icon: ⚡
24 |     title: Powerful Abstractions
25 |     details: >
26 |       Express idiomatic workflow execution patterns such as conditional execution,
27 |       dynamic resource allocation, and scatter-gather operations with ease.
28 |   - icon: 📖
29 |     title: Open Standard
30 |     details: >
31 |       WDL is collectively designed and developed by a distributed, open community. Join
32 |       Slack or participate on GitHub to have your voice heard in that process!
33 | ---
34 | 


--------------------------------------------------------------------------------
/language-guide/imports.md:
--------------------------------------------------------------------------------
 1 | # Imports
 2 | 
 3 | Often, it is desirable to split WDL code between multiple files. For example, you may
 4 | have several common tasks that you want to share between multiple workflows. In these
 5 | cases, you can use `import` statements ([spec link][spec-import-statements]) to refer to
 6 | code across files.
 7 | 
 8 | The most important bits to understand are:
 9 | 
10 | * Imports get their own namespace within WDL files,
11 | * Imports can be local files or URLs (technically, arbitrary URIs),
12 | * Imported documents **must** be the same version as the current document, and
13 | * You may alias imports or their constituent parts to avoid name collisions.
14 | 
15 | The example below shows some representative imports with brief descriptions of each.
16 | 
17 | ```wdl
18 | # Importing from a file `foo.wdl` with the namespace `foo`.
19 | import "foo.wdl"
20 | 
21 | # Importing form a file `bar.wdl` but defining its namespace as `baz`.
22 | import "bar.wdl" as baz
23 | 
24 | # Importing the `Person` struct from `person.wdl` directly into the
25 | # current namespace with the name `Individual`..
26 | import "person.wdl" alias Person as Individual 
27 | 
28 | # Importing from a URI.
29 | import "http://example.com/lib/stdlib.wdl"
30 | ```
31 | 
32 | [spec-import-statements]:
33 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#import-statements
34 | 


--------------------------------------------------------------------------------
/language-guide/structs.md:
--------------------------------------------------------------------------------
 1 | # Structs
 2 | 
 3 | **Structs** ([spec link][spec-structs]) represent custom types that you can define an
 4 | pass around within WDL. Structs are comprised of _member_ fields that have a name and an
 5 | associated type. The use of these custom types in more complex situations allows the
 6 | execution engine to do validation on your behalf, ensuring that your task or workflow
 7 | has all the information it needs in a packaged unit to run smoothly.
 8 | 
 9 | For example, consider a situation where you need to model an `Address` and some broader
10 | `ContactInformation`.
11 | 
12 | ```wdl
13 | # Create a custom type named `Address`.
14 | struct Address {
15 |   Int street_number
16 |   String street_address
17 |   Array[Int] zip_code
18 |   String city
19 |   String state
20 |   Array[Int]+? gate_code
21 | }
22 | 
23 | # Create a custom type named `ContactInformation`. It can contain
24 | # other structs, like it does here with the `address` field.
25 | struct ContactInformation {
26 |   String first_name
27 |   String last_name
28 |   Address address
29 |   String? email_address
30 | }
31 | 
32 | # An example workflow using these structs.
33 | workflow run {
34 |   output {
35 |     ContactInformation john = ContactInformation {
36 |       first_name: "John",
37 |       last_name: "Smith",
38 |       address: Address {
39 |         street_number: 123,
40 |         street_address: "Main Street",
41 |         zip_code: [0, 1, 2, 3, 4 ],
42 |         city: "Somewhere",
43 |         state: "Foobar",
44 |         gate_code: None,
45 |       },
46 |     }
47 | 
48 |     Boolean has_email = defined(john.email_address)
49 |   }
50 | }
51 | ```
52 | 
53 | To conclude, structs are an idiomatic mechanism for packaging up complex pieces of data
54 | that need to be passed around as a unit: we highly recommend you use them when you can.
55 | 
56 | [spec-structs]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#custom-types-structs
57 | 


--------------------------------------------------------------------------------
/language-guide/tasks.md:
--------------------------------------------------------------------------------
  1 | ---
  2 | outline: deep
  3 | ---
  4 | 
  5 | # Tasks
  6 | 
  7 | **Tasks** ([spec link][spec-tasks]) are the atomic unit of computation within WDL.
  8 | Fundamentally, the represent a bash script that is intended to be run to accomplish some
  9 | goal. You'll reach for tasks when defining each of the constituent analyses within a
 10 | broader [workflow](./workflows.md).
 11 | 
 12 | Tasks have a required ```command``` section and several optional sections for things
 13 | like defining inputs, defining outputs, documenting your task, and specifying runtime
 14 | requirements. We'll cover each of these in detail here while leaving an exhaustive
 15 | explanation to [the specification][spec-tasks]. 
 16 | 
 17 | Below is a representative example of what a simple task might look like.
 18 | 
 19 | ```wdl
 20 | task say_hello {
 21 |   input {
 22 |     String greeting
 23 |     String name
 24 |   }
 25 | 
 26 |   command <<<
 27 |     echo "~{greeting}, ~{name}!"
 28 |   >>>
 29 | 
 30 |   output {
 31 |     String message = read_string(stdout())
 32 |   }
 33 | 
 34 |   requirements {
 35 |     container: "ubuntu:latest"
 36 |   }
 37 | }
 38 | ```
 39 | 
 40 | ### The `command` section
 41 | 
 42 | The most important part of a task (and the only _required_ section) is the `command`
 43 | section. The command section is simply a Bash script that should be executed when the
 44 | task is run. As you can see in the snippet below, variables from within WDL can be
 45 | injected into the Bash script at runtime using the `~{variable_name}` syntax.
 46 | 
 47 | ```wdl
 48 | task say_hello {
 49 |   input {
 50 |     String greeting
 51 |     String name
 52 |   }
 53 | 
 54 |   command <<<
 55 |     echo "~{greeting}, ~{name}!"
 56 |   >>>
 57 | 
 58 |   # ...
 59 | }
 60 | ```
 61 | 
 62 | ### The `input` section
 63 | 
 64 | You can pass inputs to your task using the `input` section ([spec
 65 | link][spec-task-inputs]). Task inputs are declared as WDL variables and are generally
 66 | intended to be used as (a) values to be interpolated within the `command` section or (b)
 67 | values that are manipulated and passed through directly to the `output` section.
 68 | Variables, and how they might be declared in `input` sections, are more fully covered in
 69 | the [Variables](./variables.md#declarations) section of the language guide.
 70 | 
 71 | ### The `output` section
 72 | 
 73 | Similarly, you can declare outputs from your task using the `output` section ([spec
 74 | link][spec-task-outputs]). Outputs are generally gathered by either (a) using one or
 75 | more standard library functions to collect output from the tasks execution directory or
 76 | (b) referring to other variables directly.
 77 | 
 78 | ```wdl
 79 | task run {
 80 |   # ...
 81 | 
 82 |   output {
 83 |     # Reads an integer from a file called `threshold.txt`.
 84 |     Int threshold = read_int("threshold.txt")
 85 | 
 86 |     # Gathers a list of CSV files from the task's execution directory.
 87 |     Array[File]+ csvs = glob("*.csv")
 88 | 
 89 |     # Examines an existing variable to evaluate a boolean expression.
 90 |     Boolean two_csvs = length(csvs) == 2
 91 |   }
 92 | }
 93 | ```
 94 | 
 95 | Again, variables and the way they can be declared in `output` sections are more fully
 96 | covered in the [Variables](./variables.md#declarations) section of the language guide.
 97 | 
 98 | ### The `requirements` section
 99 | 
100 | The `requirements` section ([spec link][spec-requirements]) allows you to specify
101 | runtime requirements for a task. By far the most common use of `requirements` is to
102 | specify a [container][container-explanation] for your task to run within. This ensure
103 | that the task remains portable across multiple execution environments and is always
104 | recommended. That being said, a whole host of [`requirements`
105 | attributes][spec-requirements-attributes] exist. These cover a wide range of concepts
106 | from things like the amount resources required to run the job (e.g., the number of
107 | required cores, the amount of RAM, the amount of disk space) all the way to the valid
108 | exit codes for the job.
109 | 
110 | ```wdl
111 | task run {
112 |   # ...
113 | 
114 |   requirements {
115 |     # Constrain the container within which this task should run.
116 |     container: "ubuntu:latest",
117 | 
118 |     # Ensure that 8 cores are requisitioned.
119 |     cpu: 8,
120 | 
121 |     # Request 16 gibibytes of random-access memory.
122 |     memory: "16 GiB",
123 |   }
124 | }
125 | ```
126 | 
127 | Because this list is evolving relatively rapidly, we recommend that you go take a look
128 | at the currently supported attributes [in the specification
129 | directly][spec-requirements-attributes] to ensure you know what can be specified.
130 | 
131 | ### Documentation and metadata
132 | 
133 | Last, documentation and other metadata for your tasks is generally written in the `meta`
134 | ([spec link][spec-meta]) and `parameter_meta` ([spec link][spec-parameter-meta])
135 | sections.
136 | 
137 | * `meta` contains information related to _the task itself_. It's structured as an object
138 |   of key-values pairs that you can define for various metadata attributes of your task.
139 | * `parameter_meta` contains information related to _the inputs and outputs of the task_.
140 |   It's also structured as an object of key-values pairs, but each key _must_ correspond
141 |   to one of the inputs or outputs of the task.
142 | 
143 | At present, there is no defined standard for which keys should exist: keys are typically
144 | added by convention for each code base and/or tool that utilizes them. Future versions
145 | of WDL may consider defining conventional keys for different concepts. Below is a
146 | representative example of what a `meta` and `parameter_meta` section might look like in
147 | a task.
148 | 
149 | ```wdl
150 | task run {
151 |   # ...
152 | 
153 |   meta {
154 |     authors: ["Foo Bar <foo@bar.com>", "Baz Quux <baz@quux.com>"],
155 |     description: "This is a task that accomplishes ...",
156 |   }
157 | 
158 |   parameter_meta {
159 |     in: {
160 |       help: "The `in` parameter defines an input file that is used to ..."
161 |     },
162 |     out: {
163 |       help: "The `out` parameter defines an output file that contains ..."
164 |     }
165 |   }
166 | 
167 |   # ...
168 | }
169 | ```
170 | 
171 | ### Other sections
172 | 
173 | The above sections cover the most commonly used sections within tasks. Importantly,
174 | other concepts in the `task` section exist, such as the `hints` section ([spec
175 | link][spec-hints]), the use of private declarations ([spec link][spec-declarations]),
176 | and the use of `env` input variables ([spec link][spec-env-variables]). These are more
177 | reserved for more niche use-cases, but users may refer to the spec to learn how to use
178 | them when the need arises.
179 | 
180 | [spec-tasks]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#task-definition
181 | [spec-task-inputs]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#task-inputs
182 | [spec-task-inputs]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#task-outputs
183 | [spec-requirements]:
184 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-requirements-section
185 | [spec-requirements-attributes]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#requirements-attributes
186 | [container-explanation]:
187 |     https://azure.microsoft.com/en-us/resources/cloud-computing-dictionary/what-is-a-container/
188 | [spec-meta]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#meta-values
189 | [spec-parameter-meta]:
190 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#parameter-metadata-section
191 | [spec-hints]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-hints-section
192 | [spec-env-variables]:
193 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#environment-variables
194 | [spec-declarations]:
195 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#private-declarations
196 | 


--------------------------------------------------------------------------------
/language-guide/variables.md:
--------------------------------------------------------------------------------
  1 | ---
  2 | outline: deep
  3 | ---
  4 | 
  5 | # Variables
  6 | 
  7 | WDL supports the creation and manipulation of variables within the computation
  8 | graph. Each variable can have either a _primitive_ type or a _compound_ types.
  9 | Types may also be _optional_ meaning that they may or may not have a proper
 10 | value (i.e., their value is `None`).
 11 | 
 12 | ### Declarations
 13 | 
 14 | Variables are generally created and assigned through **declarations** ([spec
 15 | link][spec-declarations]). Briefly, if a variable is assigned to, the declaration is
 16 | known as a _bound_ declaration. If the variable is _not_ assigned, the declaration is
 17 | known as an _unbound_ declaration.
 18 | 
 19 | Bound and unbound declarations may be used in various contexts within WDL as laid out in
 20 | the specification. While a complete review of these rules is left to the specification,
 21 | a quick example should give a sense of how variables are intended to be declared and
 22 | assigned.
 23 | 
 24 | ```wdl
 25 | workflow run {
 26 |   # Inputs may have either bound or unbound inputs. Bound inputs
 27 |   # represent default values for the variable.
 28 |   input {
 29 |     # `radius` is defined in an _unbound_ declaration. The value must
 30 |     # be supplied by the caller of the workflow.
 31 |     Int radius
 32 | 
 33 |     # `pi` is defined in a _bound_ declaration. It has a default value
 34 |     # of `3.14`, but that value may be overridden by the caller.
 35 |     Float pi = 3.14
 36 | 
 37 |     # `reference` here is an _optional_ variable. It may be provided
 38 |     # by the caller, but it will have `None` as the value otherwise.
 39 |     File? reference
 40 |   }
 41 | 
 42 |   # A private declaration can be declared within a workflow or task,
 43 |   # but it must be bound.
 44 |   Int three = 1 + 2
 45 | 
 46 |   output {
 47 |     # Output declarations, such as `six` must also be bound.
 48 |     Float six = 2 * three
 49 |   }
 50 | }
 51 | ```
 52 | 
 53 | ### Primitive types
 54 | 
 55 | **Primitive types** ([spec link][spec-primitive-types]) are the base types that
 56 | variables can take. The specification defines the following primitive types:
 57 | 
 58 | * A `Boolean` represents `true` or `false`.
 59 | * An `Int` represents a 64-bit signed integer.
 60 | * A `Float` represents a 64-bit IEEE-754 floating point number.
 61 | * A `String` represents a unicode character string following the format described
 62 |   [here][spec-strings].
 63 | * A `File` represents a file (or file-like object)
 64 | * A `Directory` represents a (possibly nested) directory of files.
 65 | 
 66 | ### Optional types
 67 | 
 68 | Types that have a `?` postfix quantifier are declared as **optional types** ([spec
 69 | link][spec-optional-types]), meaning that they can also take the special value of
 70 | `None`. This concept is useful if, for example, you have optional inputs to a workflow
 71 | or you only produce some output if a particular operation mode is turned on. There are
 72 | many facilities to interact with an inspect optional types, such as the [`defined`] and
 73 | [`select_first`] standard library functions.
 74 | 
 75 | ### Compound types
 76 | 
 77 | **Compound types** ([spec link][spec-primitive-types]) are higher-order types that
 78 | organize other types in useful ways. The specification defines the following compound
 79 | types:
 80 | 
 81 | * A `Array[X]` represents an ordered list of elements of the same type ([spec
 82 |   link][spec-arrays]).
 83 | * A `Pair[X, Y]` represents two associated values ([spec link][spec-pairs]) that are
 84 |   permitted to have different types.
 85 | * A `Map[X, Y]` represents an associative array of key-value pairs ([spec
 86 |   link][spec-maps]).
 87 | * 🗑 An `Object` represents an unordered associative array of name-value pairs ([spec
 88 |   link][spec-maps]). Though valid WDL today, `Object`s are deprecated and are not
 89 |   suggested for future use.
 90 | 
 91 | [`defined`]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#select_first
 92 | [`select_first`]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#select_first
 93 | [spec-arrays]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#arrayx
 94 | [spec-objects]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-object 
 95 | [spec-maps]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#mapp-y
 96 | [spec-pairs]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#pairx-y
 97 | [spec-declarations]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#declarations
 98 | [spec-optional-types]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#optional-types-and-none
 99 | [spec-primitive-types]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#primitive-types
100 | [spec-strings]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#strings
101 | 


--------------------------------------------------------------------------------
/language-guide/versions.md:
--------------------------------------------------------------------------------
 1 | # Verisons
 2 | 
 3 | The Workflow Description Language has two concepts of versions within the project:
 4 | 
 5 | * The WDL _language_ has a two-number version (e.g., `1.2`). An increase in the
 6 |   minor (second) version number (e.g., `1.1` to `1.2`) indicates the addition
 7 |   of, or non-breaking changes to, the language or standard library functions. An
 8 |   increase in the major (first) version number (e.g., `1.0` to `2.0`) indicates
 9 |   that breaking changes have been made.
10 | 
11 | * The WDL _specification_ has a three-number version (e.g., `1.2.0`). The
12 |   specification version tracks the language version, but there may also be patch
13 |   releases (indicated by a change to the patch, or third, version number) that
14 |   include fixes for typos, additional examples, or non-breaking clarifications
15 |   of ambiguous language.
16 | 
17 | In general, users of WDL only need to care about the version of the WDL
18 | _language_—you'll rarely, if ever, need to care about the version of the
19 | _specification_ itself.
20 | 
21 | ## Upgrading
22 | 
23 | If you're interested in learning more about the finer details of upgrading
24 | between versions, such as what features new versions introduce, common pitfalls
25 | of upgrading, and how to get help, see the [Upgrade guide] in the Reference section.
26 | 
27 | ## Version specification
28 | 
29 | The WDL version is a statement that appears at the top of a WDL document—when included,
30 | it **must** be the first non-comment within the document.
31 | 
32 | :::tip NOTE
33 | Technically, the version statement is not _required_, but it is highly recommended that
34 | you do include it in all of your WDL documents. Omission of the version statement
35 | defaults to a very early version of the WDL specification (`draft-2`).
36 | :::
37 | 
38 | 
39 | You can specify the version of your WDL document like so:
40 | 
41 | ```wdl
42 | version 1.2
43 | 
44 | # ... other document contents ...
45 | ```
46 | 
47 | ## Compatability considerations
48 | 
49 | Documents may only import other WDL documents of the same version. This is
50 | because the imported documents are effectively comingled within their importer's
51 | context and processed holistically (instead of, for example, being compiled
52 | independently).
53 | 
54 | [Upgrade guide]: ../reference/upgrade-guide.md
55 | 


--------------------------------------------------------------------------------
/language-guide/workflows.md:
--------------------------------------------------------------------------------
  1 | ---
  2 | outline: deep
  3 | ---
  4 | 
  5 | # Workflows
  6 | 
  7 | **Workflows** ([spec link][spec-workflows]) define the computation graph that connects
  8 | global inputs, outputs, and `tasks` together to build a comprehensive execution plan.
  9 | While tasks are focused at the atomic computational unit level, workflows are typically
 10 | concerned with how to orchestrate the execution of those tasks in a scalable manner.
 11 | 
 12 | 
 13 | ### Common sections with `task`
 14 | 
 15 | Workflows contain multiple sections that are common with `task`s, including the `input`
 16 | section, the `output` section, and the `meta` and `parameter_meta` sections. The
 17 | description of these sections are identical with `task`s and, for brevity, we will not
 18 | cover these again in this section of the guide. If you need a refresher, we recommend
 19 | you read the relevant sections in the [Tasks](tasks.md) section.
 20 | 
 21 | [spec-workflows]:
 22 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#workflow-definition
 23 | 
 24 | ### The `call` statement
 25 | 
 26 | The `call` statement ([spec link][spec-call]) directs the workflow to execute the
 27 | specified task or subworkflow. `call`-ing a task or subworkflow brings its name into
 28 | scope within the workflow such that its inputs and outputs can be connected
 29 | together—either to global inputs and outputs of the workflow or to other
 30 | tasks/subworkflows. Further, you can use the `as` keyword to avoid naming collisions
 31 | (see [this design pattern](../design-patterns/task-aliasing/) for more information).
 32 | 
 33 | Below is an example of a typical workflow that uses call statements.
 34 | 
 35 | ```wdl
 36 | task stepA {
 37 |   # ...
 38 | }
 39 | 
 40 | task stepB {
 41 |   # ...
 42 | }
 43 | 
 44 | workflow run {
 45 |   # You can instruct the workflow to run `stepA` by `call`-ing it.
 46 |   call stepA {}
 47 | 
 48 |   # If there are inputs, you can include them within the brackets.
 49 |   call stepB { input: foo = bar }
 50 | 
 51 |   # Normally, if you wanted to call `stepA` again, there would be
 52 |   # a name conflict because the identifier `stepA` would be brought
 53 |   # into the workflow's scope twice. You can use the `as` keyword
 54 |   # to assign the task an alias.
 55 |   call stepA as stepA_again {}
 56 | }
 57 | ```
 58 | 
 59 | ### Non-sequentialism
 60 | 
 61 | A quick note on non-sequentialism: in the example above, tasks are not necessarily
 62 | executed in the order they are defined. For example, because `stepA_again` does not
 63 | depend on any outputs from `stepA` or `stepB`, it can be run immediately when the
 64 | workflow starts. This illustrates a broader point—defining a workflow means that you are
 65 | defining a _graph_ of computation—not a serial program to be executed. You can learn
 66 | more about this in [this section of the spec][spec-element-evaluation].
 67 | 
 68 | ### Conditional statement
 69 | 
 70 | A **conditional statement**, also known as an `if`/`else` statement ([spec
 71 | link][spec-conditional]) allows some subsection of the computation graph to
 72 | conditionally occur based on the specified condition. This is useful if, for example,
 73 | you want to support different modes of operation based on an input or optionally enable
 74 | an entire subanalysis of some data based on passing a QC threshold.
 75 | 
 76 | Building on our example above, we can see conditional statements in action.
 77 | 
 78 | ```wdl
 79 | task stepA {
 80 |   # ...
 81 | }
 82 | 
 83 | task stepB {
 84 |   # ...
 85 | }
 86 | 
 87 | workflow run {
 88 |   input {
 89 |     Boolean run_stepB
 90 |   }
 91 | 
 92 |   call stepA {}
 93 | 
 94 |   if (run_stepB) {
 95 |     call stepB { input: in = stepA.out }
 96 |   }
 97 | 
 98 |   # ...
 99 | }
100 | ```
101 | 
102 | For a bit more complicated example, the workflow below demonstrates (a) conditionally
103 | executing a "standard" or "alternate" mode for `stepA` and then (b) only running `stepB`
104 | if some QC metric from either mode passes.
105 | 
106 | ```wdl
107 | task stepA {
108 |   # ...
109 | }
110 | 
111 | task stepA_alternate {
112 |   # ...
113 | }
114 | 
115 | task stepB {
116 |   # ...
117 | }
118 | 
119 | workflow run {
120 |   input {
121 |     # `alternate_execution_mode` is a required workflow input.
122 |     Boolean alternate_execution_mode
123 |   }
124 | 
125 |     # Based on the value passed in as an input, either...
126 |     if (alternate_execution_mode) {
127 |         # the alternate execution mode will run, or...
128 |         call stepA_alternate {
129 |         }
130 |     }
131 | 
132 |     if (!alternate_execution_mode) {
133 |         # the standard execution mode will run...
134 |         call stepA {
135 |         }
136 |     }
137 | 
138 |     # Using `select_first`, we can pick up an output named `qc_passed`
139 |     # in either `stepA` or `stepA_alternate` (whichever ran) and then
140 |     # conditionally run `stepB` based on that result.
141 |     if (select_first([
142 |         stepA.qc_passed,
143 |         stepA_alternate.qc_passed,
144 |     ])) {
145 |         call stepB {}
146 |     }
147 | 
148 |     # ...
149 | }
150 | ```
151 | 
152 | Note that the above example uses two `if` statements because WDL doesn't yet support
153 | `else` statements. Instead, one can achieve the same effect with two if
154 | statements and a negated conditional on the second statement.
155 | 
156 | ### Design patterns
157 | 
158 | Ensuring that your workflow takes full advantage of parallelism is critical to ensuring
159 | your workflow scales well. In fact, the ease with which workflows can be defined and
160 | scaled is one of the hallmarks of the WDL language. This concept is so important that
161 | the is an entire section of the documentation titled "Design Patterns" that covers
162 | idiomatic approaches to construct workflows
163 | ([link](../design-patterns/linear-chaining/)). We highly recommend you read that section
164 | to take full advantages of the facilities WDL provides. 
165 | 
166 | [spec-call]: https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#call-statement
167 | [spec-element-evaluation]:
168 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#evaluation-of-workflow-elements
169 | [spec-conditional]:
170 |     https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#conditional-statement
171 | 


--------------------------------------------------------------------------------
/overview.md:
--------------------------------------------------------------------------------
 1 | ---
 2 | outline: deep
 3 | ---
 4 | 
 5 | # Overview
 6 | 
 7 | The **Workflow Description Language (WDL)** (pronounced as _/hwɪdl/_ or "whittle" with a
 8 | 'd') is an open standard for describing data processing workflows using a
 9 | human-readable/writeable syntax. It introduces a domain-specific language, as ratified
10 | in [the openly developed specification][specification], that aims to provide simple but
11 | powerful facilities for (a) defining atomic units of computation (a `task`), (b) for
12 | connecting those atomic units together into a larger computation graph (a `workflow`),
13 | and (c) for effortlessly scaling the execution of these graphs across multiple execution
14 | environments.
15 | 
16 | ### Values
17 | 
18 | The following are the top-level values of the project.
19 | 
20 | - **Human-readable and -writable.** WDL aims to be readable and writable by a wide
21 |   variety of audiences, including software engineers, domain experts, and platform
22 |   operators. To this end, the language prioritizes providing a concise, domain-specific
23 |   grammar that expresses the majority of (but not all) workflows succinctly. This
24 |   simplicity is the hallmark of WDL and contrasts with many other modern workflow
25 |   languages that aim for enhanced flexibility at the cost of complexity.
26 | - **Powerful abstractions.** WDL aims to be "batteries included" by exposing idiomatic
27 |   workflow execution abstractions directly within the language. Concepts such
28 |   as conditional execution, dynamic resource allocation, and scatter-gather operations
29 |   are easy to understand and express in your workflows. Further, WDL includes a
30 |   comprehensive standard library of common functions.
31 | - **Community-driven, open standard.** WDL is collectively designed and developed by a
32 |   number of distributed community members via an open process. This means you can
33 |   develop with confidence knowing that the foundation you build on will remain open in
34 |   perpetuity. It also means that _you_ can participate in the community make sure WDL is
35 |   as good as it can be! Join Slack or participate on GitHub to have your voice heard in
36 |   that process (see the [Contributing][contributing] section to learn more).
37 | 
38 | WDL also maintains a list of other values that are adhered to when possible, but not at
39 | the cost of the top-level values above.
40 | 
41 | - **Portability.** WDL aims to be portable—if your task or workflow conforms to the WDL
42 |   specification, it should run on any platform supported by your execution engine of
43 |   choice. This is particularly true if you enable [one of the LSP
44 |   integrations](./getting-started/ecosystem.md#ide-support) in your editor and follow
45 |   the portability related lints.
46 | 
47 | ### Antivalues
48 | 
49 | The following are explicitly _not_ values of the WDL language.
50 | 
51 | - _Flexibility at all costs._ WDL is a domain-specific language for expressing
52 |   computation graphs—it is not, itself, a programming language, nor is it embedded
53 |   within an existing programming language. This is an intentional decision to make WDL
54 |   more accessible to non-software engineers. That being said, the downside of that
55 |   decision is that arbitrary execution patterns cannot be expressed in WDL. If you find
56 |   yourself wanting more flexibility at the cost of added complexity, you're probably
57 |   better off using a workflow language that functions more like a programming language,
58 |   such as [Nextflow] or [Snakemake].
59 | 
60 | ### Where to start
61 | 
62 | If you're just getting started with WDL, we recommend you do a couple of things to
63 | ensure you have the best possible experience:
64 | 
65 | * Follow the quickstart guide to learn the most important concepts in WDL
66 |   ([link](./getting-started/quickstart.md)).
67 | * Install an developer extension within LSP integration, such as
68 |   [Sprocket][sprocket-ext], and pay attention to the validation errors and lints.
69 | * Select an execution engine for the environment(s) you're planning to run your
70 |   workflows within and stick with it
71 |   ([link](./getting-started/ecosystem.md#execution-engines))—contributing issues and ideas to these
72 |   engines will ultimately improve the experience for everyone!
73 | * Join Slack to get help and participate in the broader community ([link][slack-invite]).
74 | 
75 | Happy workflowing 👋!
76 | 
77 | [contributing]: ./getting-started/contributing.md
78 | [Nextflow]: https://nextflow.io 
79 | [Snakemake]: https://snakemake.readthedocs.io/en/stable
80 | [specification]: https://github.com/openwdl/wdl
81 | [sprocket-ext]:
82 |     https://marketplace.visualstudio.com/items?itemName=stjude-rust-labs.sprocket-vscode
83 | [slack-invite]:
84 |     https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw
85 | 


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  59 | 
  60 |   '@algolia/client-query-suggestions@5.19.0':
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  63 | 
  64 |   '@algolia/client-search@5.19.0':
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  67 | 
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  72 |   '@algolia/monitoring@1.19.0':
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  74 |     engines: {node: '>= 14.0.0'}
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  76 |   '@algolia/recommend@5.19.0':
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  78 |     engines: {node: '>= 14.0.0'}
  79 | 
  80 |   '@algolia/requester-browser-xhr@5.19.0':
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  83 | 
  84 |   '@algolia/requester-fetch@5.19.0':
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  86 |     engines: {node: '>= 14.0.0'}
  87 | 
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  90 |     engines: {node: '>= 14.0.0'}
  91 | 
  92 |   '@babel/helper-string-parser@7.25.9':
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  98 |     engines: {node: '>=6.9.0'}
  99 | 
 100 |   '@babel/parser@7.26.5':
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 102 |     engines: {node: '>=6.0.0'}
 103 |     hasBin: true
 104 | 
 105 |   '@babel/types@7.26.5':
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 107 |     engines: {node: '>=6.9.0'}
 108 | 
 109 |   '@docsearch/css@3.8.2':
 110 |     resolution: {integrity: sha512-y05ayQFyUmCXze79+56v/4HpycYF3uFqB78pLPrSV5ZKAlDuIAAJNhaRi8tTdRNXh05yxX/TyNnzD6LwSM89vQ==}
 111 | 
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 114 | 
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 117 |     peerDependencies:
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 120 |       react-dom: '>= 16.8.0 < 19.0.0'
 121 |       search-insights: '>= 1 < 3'
 122 |     peerDependenciesMeta:
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 125 |       react:
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 127 |       react-dom:
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 184 |     os: [linux]
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 186 |   '@esbuild/linux-arm@0.21.5':
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 188 |     engines: {node: '>=12'}
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 204 |   '@esbuild/linux-mips64el@0.21.5':
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 245 | 
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 248 |     engines: {node: '>=12'}
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 250 |     os: [sunos]
 251 | 
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 254 |     engines: {node: '>=12'}
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 257 | 
 258 |   '@esbuild/win32-ia32@0.21.5':
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 260 |     engines: {node: '>=12'}
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 263 | 
 264 |   '@esbuild/win32-x64@0.21.5':
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 268 |     os: [win32]
 269 | 
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 275 | 
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 278 | 
 279 |   '@rollup/rollup-android-arm-eabi@4.30.1':
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 296 |     cpu: [x64]
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 303 | 
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 306 |     cpu: [x64]
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 308 | 
 309 |   '@rollup/rollup-linux-arm-gnueabihf@4.30.1':
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 313 | 
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 317 |     os: [linux]
 318 | 
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 323 | 
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 333 | 
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 338 | 
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 341 |     cpu: [riscv64]
 342 |     os: [linux]
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 356 |     cpu: [x64]
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 358 | 
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 363 | 
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 366 |     cpu: [ia32]
 367 |     os: [win32]
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 720 | 
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 723 |     engines: {node: '>=16'}
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 725 |   tabbable@6.2.0:
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 727 | 
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 730 | 
 731 |   unist-util-is@6.0.0:
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 733 | 
 734 |   unist-util-position@5.0.0:
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 736 | 
 737 |   unist-util-stringify-position@4.0.0:
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 739 | 
 740 |   unist-util-visit-parents@6.0.1:
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 742 | 
 743 |   unist-util-visit@5.0.0:
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 745 | 
 746 |   vfile-message@4.0.2:
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 748 | 
 749 |   vfile@6.0.3:
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 751 | 
 752 |   vite@5.4.11:
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 754 |     engines: {node: ^18.0.0 || >=20.0.0}
 755 |     hasBin: true
 756 |     peerDependencies:
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 758 |       less: '*'
 759 |       lightningcss: ^1.21.0
 760 |       sass: '*'
 761 |       sass-embedded: '*'
 762 |       stylus: '*'
 763 |       sugarss: '*'
 764 |       terser: ^5.4.0
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 768 |       less:
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 770 |       lightningcss:
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 772 |       sass:
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 774 |       sass-embedded:
 775 |         optional: true
 776 |       stylus:
 777 |         optional: true
 778 |       sugarss:
 779 |         optional: true
 780 |       terser:
 781 |         optional: true
 782 | 
 783 |   vitepress@1.5.0:
 784 |     resolution: {integrity: sha512-q4Q/G2zjvynvizdB3/bupdYkCJe2umSAMv9Ju4d92E6/NXJ59z70xB0q5p/4lpRyAwflDsbwy1mLV9Q5+nlB+g==}
 785 |     hasBin: true
 786 |     peerDependencies:
 787 |       markdown-it-mathjax3: ^4
 788 |       postcss: ^8
 789 |     peerDependenciesMeta:
 790 |       markdown-it-mathjax3:
 791 |         optional: true
 792 |       postcss:
 793 |         optional: true
 794 | 
 795 |   vue-demi@0.14.10:
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 797 |     engines: {node: '>=12'}
 798 |     hasBin: true
 799 |     peerDependencies:
 800 |       '@vue/composition-api': ^1.0.0-rc.1
 801 |       vue: ^3.0.0-0 || ^2.6.0
 802 |     peerDependenciesMeta:
 803 |       '@vue/composition-api':
 804 |         optional: true
 805 | 
 806 |   vue@3.5.13:
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 808 |     peerDependencies:
 809 |       typescript: '*'
 810 |     peerDependenciesMeta:
 811 |       typescript:
 812 |         optional: true
 813 | 
 814 |   zwitch@2.0.4:
 815 |     resolution: {integrity: sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==}
 816 | 
 817 | snapshots:
 818 | 
 819 |   '@algolia/autocomplete-core@1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)(search-insights@2.17.3)':
 820 |     dependencies:
 821 |       '@algolia/autocomplete-plugin-algolia-insights': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)(search-insights@2.17.3)
 822 |       '@algolia/autocomplete-shared': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)
 823 |     transitivePeerDependencies:
 824 |       - '@algolia/client-search'
 825 |       - algoliasearch
 826 |       - search-insights
 827 | 
 828 |   '@algolia/autocomplete-plugin-algolia-insights@1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)(search-insights@2.17.3)':
 829 |     dependencies:
 830 |       '@algolia/autocomplete-shared': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)
 831 |       search-insights: 2.17.3
 832 |     transitivePeerDependencies:
 833 |       - '@algolia/client-search'
 834 |       - algoliasearch
 835 | 
 836 |   '@algolia/autocomplete-preset-algolia@1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)':
 837 |     dependencies:
 838 |       '@algolia/autocomplete-shared': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)
 839 |       '@algolia/client-search': 5.19.0
 840 |       algoliasearch: 5.19.0
 841 | 
 842 |   '@algolia/autocomplete-shared@1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)':
 843 |     dependencies:
 844 |       '@algolia/client-search': 5.19.0
 845 |       algoliasearch: 5.19.0
 846 | 
 847 |   '@algolia/client-abtesting@5.19.0':
 848 |     dependencies:
 849 |       '@algolia/client-common': 5.19.0
 850 |       '@algolia/requester-browser-xhr': 5.19.0
 851 |       '@algolia/requester-fetch': 5.19.0
 852 |       '@algolia/requester-node-http': 5.19.0
 853 | 
 854 |   '@algolia/client-analytics@5.19.0':
 855 |     dependencies:
 856 |       '@algolia/client-common': 5.19.0
 857 |       '@algolia/requester-browser-xhr': 5.19.0
 858 |       '@algolia/requester-fetch': 5.19.0
 859 |       '@algolia/requester-node-http': 5.19.0
 860 | 
 861 |   '@algolia/client-common@5.19.0': {}
 862 | 
 863 |   '@algolia/client-insights@5.19.0':
 864 |     dependencies:
 865 |       '@algolia/client-common': 5.19.0
 866 |       '@algolia/requester-browser-xhr': 5.19.0
 867 |       '@algolia/requester-fetch': 5.19.0
 868 |       '@algolia/requester-node-http': 5.19.0
 869 | 
 870 |   '@algolia/client-personalization@5.19.0':
 871 |     dependencies:
 872 |       '@algolia/client-common': 5.19.0
 873 |       '@algolia/requester-browser-xhr': 5.19.0
 874 |       '@algolia/requester-fetch': 5.19.0
 875 |       '@algolia/requester-node-http': 5.19.0
 876 | 
 877 |   '@algolia/client-query-suggestions@5.19.0':
 878 |     dependencies:
 879 |       '@algolia/client-common': 5.19.0
 880 |       '@algolia/requester-browser-xhr': 5.19.0
 881 |       '@algolia/requester-fetch': 5.19.0
 882 |       '@algolia/requester-node-http': 5.19.0
 883 | 
 884 |   '@algolia/client-search@5.19.0':
 885 |     dependencies:
 886 |       '@algolia/client-common': 5.19.0
 887 |       '@algolia/requester-browser-xhr': 5.19.0
 888 |       '@algolia/requester-fetch': 5.19.0
 889 |       '@algolia/requester-node-http': 5.19.0
 890 | 
 891 |   '@algolia/ingestion@1.19.0':
 892 |     dependencies:
 893 |       '@algolia/client-common': 5.19.0
 894 |       '@algolia/requester-browser-xhr': 5.19.0
 895 |       '@algolia/requester-fetch': 5.19.0
 896 |       '@algolia/requester-node-http': 5.19.0
 897 | 
 898 |   '@algolia/monitoring@1.19.0':
 899 |     dependencies:
 900 |       '@algolia/client-common': 5.19.0
 901 |       '@algolia/requester-browser-xhr': 5.19.0
 902 |       '@algolia/requester-fetch': 5.19.0
 903 |       '@algolia/requester-node-http': 5.19.0
 904 | 
 905 |   '@algolia/recommend@5.19.0':
 906 |     dependencies:
 907 |       '@algolia/client-common': 5.19.0
 908 |       '@algolia/requester-browser-xhr': 5.19.0
 909 |       '@algolia/requester-fetch': 5.19.0
 910 |       '@algolia/requester-node-http': 5.19.0
 911 | 
 912 |   '@algolia/requester-browser-xhr@5.19.0':
 913 |     dependencies:
 914 |       '@algolia/client-common': 5.19.0
 915 | 
 916 |   '@algolia/requester-fetch@5.19.0':
 917 |     dependencies:
 918 |       '@algolia/client-common': 5.19.0
 919 | 
 920 |   '@algolia/requester-node-http@5.19.0':
 921 |     dependencies:
 922 |       '@algolia/client-common': 5.19.0
 923 | 
 924 |   '@babel/helper-string-parser@7.25.9': {}
 925 | 
 926 |   '@babel/helper-validator-identifier@7.25.9': {}
 927 | 
 928 |   '@babel/parser@7.26.5':
 929 |     dependencies:
 930 |       '@babel/types': 7.26.5
 931 | 
 932 |   '@babel/types@7.26.5':
 933 |     dependencies:
 934 |       '@babel/helper-string-parser': 7.25.9
 935 |       '@babel/helper-validator-identifier': 7.25.9
 936 | 
 937 |   '@docsearch/css@3.8.2': {}
 938 | 
 939 |   '@docsearch/js@3.8.2(@algolia/client-search@5.19.0)(search-insights@2.17.3)':
 940 |     dependencies:
 941 |       '@docsearch/react': 3.8.2(@algolia/client-search@5.19.0)(search-insights@2.17.3)
 942 |       preact: 10.25.4
 943 |     transitivePeerDependencies:
 944 |       - '@algolia/client-search'
 945 |       - '@types/react'
 946 |       - react
 947 |       - react-dom
 948 |       - search-insights
 949 | 
 950 |   '@docsearch/react@3.8.2(@algolia/client-search@5.19.0)(search-insights@2.17.3)':
 951 |     dependencies:
 952 |       '@algolia/autocomplete-core': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)(search-insights@2.17.3)
 953 |       '@algolia/autocomplete-preset-algolia': 1.17.7(@algolia/client-search@5.19.0)(algoliasearch@5.19.0)
 954 |       '@docsearch/css': 3.8.2
 955 |       algoliasearch: 5.19.0
 956 |     optionalDependencies:
 957 |       search-insights: 2.17.3
 958 |     transitivePeerDependencies:
 959 |       - '@algolia/client-search'
 960 | 
 961 |   '@esbuild/aix-ppc64@0.21.5':
 962 |     optional: true
 963 | 
 964 |   '@esbuild/android-arm64@0.21.5':
 965 |     optional: true
 966 | 
 967 |   '@esbuild/android-arm@0.21.5':
 968 |     optional: true
 969 | 
 970 |   '@esbuild/android-x64@0.21.5':
 971 |     optional: true
 972 | 
 973 |   '@esbuild/darwin-arm64@0.21.5':
 974 |     optional: true
 975 | 
 976 |   '@esbuild/darwin-x64@0.21.5':
 977 |     optional: true
 978 | 
 979 |   '@esbuild/freebsd-arm64@0.21.5':
 980 |     optional: true
 981 | 
 982 |   '@esbuild/freebsd-x64@0.21.5':
 983 |     optional: true
 984 | 
 985 |   '@esbuild/linux-arm64@0.21.5':
 986 |     optional: true
 987 | 
 988 |   '@esbuild/linux-arm@0.21.5':
 989 |     optional: true
 990 | 
 991 |   '@esbuild/linux-ia32@0.21.5':
 992 |     optional: true
 993 | 
 994 |   '@esbuild/linux-loong64@0.21.5':
 995 |     optional: true
 996 | 
 997 |   '@esbuild/linux-mips64el@0.21.5':
 998 |     optional: true
 999 | 
1000 |   '@esbuild/linux-ppc64@0.21.5':
1001 |     optional: true
1002 | 
1003 |   '@esbuild/linux-riscv64@0.21.5':
1004 |     optional: true
1005 | 
1006 |   '@esbuild/linux-s390x@0.21.5':
1007 |     optional: true
1008 | 
1009 |   '@esbuild/linux-x64@0.21.5':
1010 |     optional: true
1011 | 
1012 |   '@esbuild/netbsd-x64@0.21.5':
1013 |     optional: true
1014 | 
1015 |   '@esbuild/openbsd-x64@0.21.5':
1016 |     optional: true
1017 | 
1018 |   '@esbuild/sunos-x64@0.21.5':
1019 |     optional: true
1020 | 
1021 |   '@esbuild/win32-arm64@0.21.5':
1022 |     optional: true
1023 | 
1024 |   '@esbuild/win32-ia32@0.21.5':
1025 |     optional: true
1026 | 
1027 |   '@esbuild/win32-x64@0.21.5':
1028 |     optional: true
1029 | 
1030 |   '@iconify-json/simple-icons@1.2.19':
1031 |     dependencies:
1032 |       '@iconify/types': 2.0.0
1033 | 
1034 |   '@iconify/types@2.0.0': {}
1035 | 
1036 |   '@jridgewell/sourcemap-codec@1.5.0': {}
1037 | 
1038 |   '@rollup/rollup-android-arm-eabi@4.30.1':
1039 |     optional: true
1040 | 
1041 |   '@rollup/rollup-android-arm64@4.30.1':
1042 |     optional: true
1043 | 
1044 |   '@rollup/rollup-darwin-arm64@4.30.1':
1045 |     optional: true
1046 | 
1047 |   '@rollup/rollup-darwin-x64@4.30.1':
1048 |     optional: true
1049 | 
1050 |   '@rollup/rollup-freebsd-arm64@4.30.1':
1051 |     optional: true
1052 | 
1053 |   '@rollup/rollup-freebsd-x64@4.30.1':
1054 |     optional: true
1055 | 
1056 |   '@rollup/rollup-linux-arm-gnueabihf@4.30.1':
1057 |     optional: true
1058 | 
1059 |   '@rollup/rollup-linux-arm-musleabihf@4.30.1':
1060 |     optional: true
1061 | 
1062 |   '@rollup/rollup-linux-arm64-gnu@4.30.1':
1063 |     optional: true
1064 | 
1065 |   '@rollup/rollup-linux-arm64-musl@4.30.1':
1066 |     optional: true
1067 | 
1068 |   '@rollup/rollup-linux-loongarch64-gnu@4.30.1':
1069 |     optional: true
1070 | 
1071 |   '@rollup/rollup-linux-powerpc64le-gnu@4.30.1':
1072 |     optional: true
1073 | 
1074 |   '@rollup/rollup-linux-riscv64-gnu@4.30.1':
1075 |     optional: true
1076 | 
1077 |   '@rollup/rollup-linux-s390x-gnu@4.30.1':
1078 |     optional: true
1079 | 
1080 |   '@rollup/rollup-linux-x64-gnu@4.30.1':
1081 |     optional: true
1082 | 
1083 |   '@rollup/rollup-linux-x64-musl@4.30.1':
1084 |     optional: true
1085 | 
1086 |   '@rollup/rollup-win32-arm64-msvc@4.30.1':
1087 |     optional: true
1088 | 
1089 |   '@rollup/rollup-win32-ia32-msvc@4.30.1':
1090 |     optional: true
1091 | 
1092 |   '@rollup/rollup-win32-x64-msvc@4.30.1':
1093 |     optional: true
1094 | 
1095 |   '@shikijs/core@1.26.1':
1096 |     dependencies:
1097 |       '@shikijs/engine-javascript': 1.26.1
1098 |       '@shikijs/engine-oniguruma': 1.26.1
1099 |       '@shikijs/types': 1.26.1
1100 |       '@shikijs/vscode-textmate': 10.0.1
1101 |       '@types/hast': 3.0.4
1102 |       hast-util-to-html: 9.0.4
1103 | 
1104 |   '@shikijs/engine-javascript@1.26.1':
1105 |     dependencies:
1106 |       '@shikijs/types': 1.26.1
1107 |       '@shikijs/vscode-textmate': 10.0.1
1108 |       oniguruma-to-es: 0.10.0
1109 | 
1110 |   '@shikijs/engine-oniguruma@1.26.1':
1111 |     dependencies:
1112 |       '@shikijs/types': 1.26.1
1113 |       '@shikijs/vscode-textmate': 10.0.1
1114 | 
1115 |   '@shikijs/langs@1.26.1':
1116 |     dependencies:
1117 |       '@shikijs/types': 1.26.1
1118 | 
1119 |   '@shikijs/themes@1.26.1':
1120 |     dependencies:
1121 |       '@shikijs/types': 1.26.1
1122 | 
1123 |   '@shikijs/transformers@1.26.1':
1124 |     dependencies:
1125 |       shiki: 1.26.1
1126 | 
1127 |   '@shikijs/types@1.26.1':
1128 |     dependencies:
1129 |       '@shikijs/vscode-textmate': 10.0.1
1130 |       '@types/hast': 3.0.4
1131 | 
1132 |   '@shikijs/vscode-textmate@10.0.1': {}
1133 | 
1134 |   '@types/estree@1.0.6': {}
1135 | 
1136 |   '@types/hast@3.0.4':
1137 |     dependencies:
1138 |       '@types/unist': 3.0.3
1139 | 
1140 |   '@types/linkify-it@5.0.0': {}
1141 | 
1142 |   '@types/markdown-it@14.1.2':
1143 |     dependencies:
1144 |       '@types/linkify-it': 5.0.0
1145 |       '@types/mdurl': 2.0.0
1146 | 
1147 |   '@types/mdast@4.0.4':
1148 |     dependencies:
1149 |       '@types/unist': 3.0.3
1150 | 
1151 |   '@types/mdurl@2.0.0': {}
1152 | 
1153 |   '@types/unist@3.0.3': {}
1154 | 
1155 |   '@types/web-bluetooth@0.0.20': {}
1156 | 
1157 |   '@ungap/structured-clone@1.2.1': {}
1158 | 
1159 |   '@vitejs/plugin-vue@5.2.1(vite@5.4.11)(vue@3.5.13)':
1160 |     dependencies:
1161 |       vite: 5.4.11
1162 |       vue: 3.5.13
1163 | 
1164 |   '@vue/compiler-core@3.5.13':
1165 |     dependencies:
1166 |       '@babel/parser': 7.26.5
1167 |       '@vue/shared': 3.5.13
1168 |       entities: 4.5.0
1169 |       estree-walker: 2.0.2
1170 |       source-map-js: 1.2.1
1171 | 
1172 |   '@vue/compiler-dom@3.5.13':
1173 |     dependencies:
1174 |       '@vue/compiler-core': 3.5.13
1175 |       '@vue/shared': 3.5.13
1176 | 
1177 |   '@vue/compiler-sfc@3.5.13':
1178 |     dependencies:
1179 |       '@babel/parser': 7.26.5
1180 |       '@vue/compiler-core': 3.5.13
1181 |       '@vue/compiler-dom': 3.5.13
1182 |       '@vue/compiler-ssr': 3.5.13
1183 |       '@vue/shared': 3.5.13
1184 |       estree-walker: 2.0.2
1185 |       magic-string: 0.30.17
1186 |       postcss: 8.4.49
1187 |       source-map-js: 1.2.1
1188 | 
1189 |   '@vue/compiler-ssr@3.5.13':
1190 |     dependencies:
1191 |       '@vue/compiler-dom': 3.5.13
1192 |       '@vue/shared': 3.5.13
1193 | 
1194 |   '@vue/devtools-api@7.7.0':
1195 |     dependencies:
1196 |       '@vue/devtools-kit': 7.7.0
1197 | 
1198 |   '@vue/devtools-kit@7.7.0':
1199 |     dependencies:
1200 |       '@vue/devtools-shared': 7.7.0
1201 |       birpc: 0.2.19
1202 |       hookable: 5.5.3
1203 |       mitt: 3.0.1
1204 |       perfect-debounce: 1.0.0
1205 |       speakingurl: 14.0.1
1206 |       superjson: 2.2.2
1207 | 
1208 |   '@vue/devtools-shared@7.7.0':
1209 |     dependencies:
1210 |       rfdc: 1.4.1
1211 | 
1212 |   '@vue/reactivity@3.5.13':
1213 |     dependencies:
1214 |       '@vue/shared': 3.5.13
1215 | 
1216 |   '@vue/runtime-core@3.5.13':
1217 |     dependencies:
1218 |       '@vue/reactivity': 3.5.13
1219 |       '@vue/shared': 3.5.13
1220 | 
1221 |   '@vue/runtime-dom@3.5.13':
1222 |     dependencies:
1223 |       '@vue/reactivity': 3.5.13
1224 |       '@vue/runtime-core': 3.5.13
1225 |       '@vue/shared': 3.5.13
1226 |       csstype: 3.1.3
1227 | 
1228 |   '@vue/server-renderer@3.5.13(vue@3.5.13)':
1229 |     dependencies:
1230 |       '@vue/compiler-ssr': 3.5.13
1231 |       '@vue/shared': 3.5.13
1232 |       vue: 3.5.13
1233 | 
1234 |   '@vue/shared@3.5.13': {}
1235 | 
1236 |   '@vueuse/core@11.3.0(vue@3.5.13)':
1237 |     dependencies:
1238 |       '@types/web-bluetooth': 0.0.20
1239 |       '@vueuse/metadata': 11.3.0
1240 |       '@vueuse/shared': 11.3.0(vue@3.5.13)
1241 |       vue-demi: 0.14.10(vue@3.5.13)
1242 |     transitivePeerDependencies:
1243 |       - '@vue/composition-api'
1244 |       - vue
1245 | 
1246 |   '@vueuse/integrations@11.3.0(axios@1.7.9)(focus-trap@7.6.4)(vue@3.5.13)':
1247 |     dependencies:
1248 |       '@vueuse/core': 11.3.0(vue@3.5.13)
1249 |       '@vueuse/shared': 11.3.0(vue@3.5.13)
1250 |       vue-demi: 0.14.10(vue@3.5.13)
1251 |     optionalDependencies:
1252 |       axios: 1.7.9
1253 |       focus-trap: 7.6.4
1254 |     transitivePeerDependencies:
1255 |       - '@vue/composition-api'
1256 |       - vue
1257 | 
1258 |   '@vueuse/metadata@11.3.0': {}
1259 | 
1260 |   '@vueuse/shared@11.3.0(vue@3.5.13)':
1261 |     dependencies:
1262 |       vue-demi: 0.14.10(vue@3.5.13)
1263 |     transitivePeerDependencies:
1264 |       - '@vue/composition-api'
1265 |       - vue
1266 | 
1267 |   algoliasearch@5.19.0:
1268 |     dependencies:
1269 |       '@algolia/client-abtesting': 5.19.0
1270 |       '@algolia/client-analytics': 5.19.0
1271 |       '@algolia/client-common': 5.19.0
1272 |       '@algolia/client-insights': 5.19.0
1273 |       '@algolia/client-personalization': 5.19.0
1274 |       '@algolia/client-query-suggestions': 5.19.0
1275 |       '@algolia/client-search': 5.19.0
1276 |       '@algolia/ingestion': 1.19.0
1277 |       '@algolia/monitoring': 1.19.0
1278 |       '@algolia/recommend': 5.19.0
1279 |       '@algolia/requester-browser-xhr': 5.19.0
1280 |       '@algolia/requester-fetch': 5.19.0
1281 |       '@algolia/requester-node-http': 5.19.0
1282 | 
1283 |   asynckit@0.4.0: {}
1284 | 
1285 |   axios@1.7.9:
1286 |     dependencies:
1287 |       follow-redirects: 1.15.9
1288 |       form-data: 4.0.1
1289 |       proxy-from-env: 1.1.0
1290 |     transitivePeerDependencies:
1291 |       - debug
1292 | 
1293 |   birpc@0.2.19: {}
1294 | 
1295 |   ccount@2.0.1: {}
1296 | 
1297 |   character-entities-html4@2.1.0: {}
1298 | 
1299 |   character-entities-legacy@3.0.0: {}
1300 | 
1301 |   combined-stream@1.0.8:
1302 |     dependencies:
1303 |       delayed-stream: 1.0.0
1304 | 
1305 |   comma-separated-tokens@2.0.3: {}
1306 | 
1307 |   copy-anything@3.0.5:
1308 |     dependencies:
1309 |       is-what: 4.1.16
1310 | 
1311 |   csstype@3.1.3: {}
1312 | 
1313 |   delayed-stream@1.0.0: {}
1314 | 
1315 |   dequal@2.0.3: {}
1316 | 
1317 |   devlop@1.1.0:
1318 |     dependencies:
1319 |       dequal: 2.0.3
1320 | 
1321 |   emoji-regex-xs@1.0.0: {}
1322 | 
1323 |   entities@4.5.0: {}
1324 | 
1325 |   esbuild@0.21.5:
1326 |     optionalDependencies:
1327 |       '@esbuild/aix-ppc64': 0.21.5
1328 |       '@esbuild/android-arm': 0.21.5
1329 |       '@esbuild/android-arm64': 0.21.5
1330 |       '@esbuild/android-x64': 0.21.5
1331 |       '@esbuild/darwin-arm64': 0.21.5
1332 |       '@esbuild/darwin-x64': 0.21.5
1333 |       '@esbuild/freebsd-arm64': 0.21.5
1334 |       '@esbuild/freebsd-x64': 0.21.5
1335 |       '@esbuild/linux-arm': 0.21.5
1336 |       '@esbuild/linux-arm64': 0.21.5
1337 |       '@esbuild/linux-ia32': 0.21.5
1338 |       '@esbuild/linux-loong64': 0.21.5
1339 |       '@esbuild/linux-mips64el': 0.21.5
1340 |       '@esbuild/linux-ppc64': 0.21.5
1341 |       '@esbuild/linux-riscv64': 0.21.5
1342 |       '@esbuild/linux-s390x': 0.21.5
1343 |       '@esbuild/linux-x64': 0.21.5
1344 |       '@esbuild/netbsd-x64': 0.21.5
1345 |       '@esbuild/openbsd-x64': 0.21.5
1346 |       '@esbuild/sunos-x64': 0.21.5
1347 |       '@esbuild/win32-arm64': 0.21.5
1348 |       '@esbuild/win32-ia32': 0.21.5
1349 |       '@esbuild/win32-x64': 0.21.5
1350 | 
1351 |   estree-walker@2.0.2: {}
1352 | 
1353 |   focus-trap@7.6.4:
1354 |     dependencies:
1355 |       tabbable: 6.2.0
1356 | 
1357 |   follow-redirects@1.15.9: {}
1358 | 
1359 |   form-data@4.0.1:
1360 |     dependencies:
1361 |       asynckit: 0.4.0
1362 |       combined-stream: 1.0.8
1363 |       mime-types: 2.1.35
1364 | 
1365 |   fsevents@2.3.3:
1366 |     optional: true
1367 | 
1368 |   hast-util-to-html@9.0.4:
1369 |     dependencies:
1370 |       '@types/hast': 3.0.4
1371 |       '@types/unist': 3.0.3
1372 |       ccount: 2.0.1
1373 |       comma-separated-tokens: 2.0.3
1374 |       hast-util-whitespace: 3.0.0
1375 |       html-void-elements: 3.0.0
1376 |       mdast-util-to-hast: 13.2.0
1377 |       property-information: 6.5.0
1378 |       space-separated-tokens: 2.0.2
1379 |       stringify-entities: 4.0.4
1380 |       zwitch: 2.0.4
1381 | 
1382 |   hast-util-whitespace@3.0.0:
1383 |     dependencies:
1384 |       '@types/hast': 3.0.4
1385 | 
1386 |   hookable@5.5.3: {}
1387 | 
1388 |   html-void-elements@3.0.0: {}
1389 | 
1390 |   is-what@4.1.16: {}
1391 | 
1392 |   magic-string@0.30.17:
1393 |     dependencies:
1394 |       '@jridgewell/sourcemap-codec': 1.5.0
1395 | 
1396 |   mark.js@8.11.1: {}
1397 | 
1398 |   mdast-util-to-hast@13.2.0:
1399 |     dependencies:
1400 |       '@types/hast': 3.0.4
1401 |       '@types/mdast': 4.0.4
1402 |       '@ungap/structured-clone': 1.2.1
1403 |       devlop: 1.1.0
1404 |       micromark-util-sanitize-uri: 2.0.1
1405 |       trim-lines: 3.0.1
1406 |       unist-util-position: 5.0.0
1407 |       unist-util-visit: 5.0.0
1408 |       vfile: 6.0.3
1409 | 
1410 |   micromark-util-character@2.1.1:
1411 |     dependencies:
1412 |       micromark-util-symbol: 2.0.1
1413 |       micromark-util-types: 2.0.1
1414 | 
1415 |   micromark-util-encode@2.0.1: {}
1416 | 
1417 |   micromark-util-sanitize-uri@2.0.1:
1418 |     dependencies:
1419 |       micromark-util-character: 2.1.1
1420 |       micromark-util-encode: 2.0.1
1421 |       micromark-util-symbol: 2.0.1
1422 | 
1423 |   micromark-util-symbol@2.0.1: {}
1424 | 
1425 |   micromark-util-types@2.0.1: {}
1426 | 
1427 |   mime-db@1.52.0: {}
1428 | 
1429 |   mime-types@2.1.35:
1430 |     dependencies:
1431 |       mime-db: 1.52.0
1432 | 
1433 |   minisearch@7.1.1: {}
1434 | 
1435 |   mitt@3.0.1: {}
1436 | 
1437 |   nanoid@3.3.8: {}
1438 | 
1439 |   oniguruma-to-es@0.10.0:
1440 |     dependencies:
1441 |       emoji-regex-xs: 1.0.0
1442 |       regex: 5.1.1
1443 |       regex-recursion: 5.1.1
1444 | 
1445 |   perfect-debounce@1.0.0: {}
1446 | 
1447 |   picocolors@1.1.1: {}
1448 | 
1449 |   postcss@8.4.49:
1450 |     dependencies:
1451 |       nanoid: 3.3.8
1452 |       picocolors: 1.1.1
1453 |       source-map-js: 1.2.1
1454 | 
1455 |   preact@10.25.4: {}
1456 | 
1457 |   property-information@6.5.0: {}
1458 | 
1459 |   proxy-from-env@1.1.0: {}
1460 | 
1461 |   regex-recursion@5.1.1:
1462 |     dependencies:
1463 |       regex: 5.1.1
1464 |       regex-utilities: 2.3.0
1465 | 
1466 |   regex-utilities@2.3.0: {}
1467 | 
1468 |   regex@5.1.1:
1469 |     dependencies:
1470 |       regex-utilities: 2.3.0
1471 | 
1472 |   rfdc@1.4.1: {}
1473 | 
1474 |   rollup@4.30.1:
1475 |     dependencies:
1476 |       '@types/estree': 1.0.6
1477 |     optionalDependencies:
1478 |       '@rollup/rollup-android-arm-eabi': 4.30.1
1479 |       '@rollup/rollup-android-arm64': 4.30.1
1480 |       '@rollup/rollup-darwin-arm64': 4.30.1
1481 |       '@rollup/rollup-darwin-x64': 4.30.1
1482 |       '@rollup/rollup-freebsd-arm64': 4.30.1
1483 |       '@rollup/rollup-freebsd-x64': 4.30.1
1484 |       '@rollup/rollup-linux-arm-gnueabihf': 4.30.1
1485 |       '@rollup/rollup-linux-arm-musleabihf': 4.30.1
1486 |       '@rollup/rollup-linux-arm64-gnu': 4.30.1
1487 |       '@rollup/rollup-linux-arm64-musl': 4.30.1
1488 |       '@rollup/rollup-linux-loongarch64-gnu': 4.30.1
1489 |       '@rollup/rollup-linux-powerpc64le-gnu': 4.30.1
1490 |       '@rollup/rollup-linux-riscv64-gnu': 4.30.1
1491 |       '@rollup/rollup-linux-s390x-gnu': 4.30.1
1492 |       '@rollup/rollup-linux-x64-gnu': 4.30.1
1493 |       '@rollup/rollup-linux-x64-musl': 4.30.1
1494 |       '@rollup/rollup-win32-arm64-msvc': 4.30.1
1495 |       '@rollup/rollup-win32-ia32-msvc': 4.30.1
1496 |       '@rollup/rollup-win32-x64-msvc': 4.30.1
1497 |       fsevents: 2.3.3
1498 | 
1499 |   search-insights@2.17.3: {}
1500 | 
1501 |   shiki@1.26.1:
1502 |     dependencies:
1503 |       '@shikijs/core': 1.26.1
1504 |       '@shikijs/engine-javascript': 1.26.1
1505 |       '@shikijs/engine-oniguruma': 1.26.1
1506 |       '@shikijs/langs': 1.26.1
1507 |       '@shikijs/themes': 1.26.1
1508 |       '@shikijs/types': 1.26.1
1509 |       '@shikijs/vscode-textmate': 10.0.1
1510 |       '@types/hast': 3.0.4
1511 | 
1512 |   source-map-js@1.2.1: {}
1513 | 
1514 |   space-separated-tokens@2.0.2: {}
1515 | 
1516 |   speakingurl@14.0.1: {}
1517 | 
1518 |   stringify-entities@4.0.4:
1519 |     dependencies:
1520 |       character-entities-html4: 2.1.0
1521 |       character-entities-legacy: 3.0.0
1522 | 
1523 |   superjson@2.2.2:
1524 |     dependencies:
1525 |       copy-anything: 3.0.5
1526 | 
1527 |   tabbable@6.2.0: {}
1528 | 
1529 |   trim-lines@3.0.1: {}
1530 | 
1531 |   unist-util-is@6.0.0:
1532 |     dependencies:
1533 |       '@types/unist': 3.0.3
1534 | 
1535 |   unist-util-position@5.0.0:
1536 |     dependencies:
1537 |       '@types/unist': 3.0.3
1538 | 
1539 |   unist-util-stringify-position@4.0.0:
1540 |     dependencies:
1541 |       '@types/unist': 3.0.3
1542 | 
1543 |   unist-util-visit-parents@6.0.1:
1544 |     dependencies:
1545 |       '@types/unist': 3.0.3
1546 |       unist-util-is: 6.0.0
1547 | 
1548 |   unist-util-visit@5.0.0:
1549 |     dependencies:
1550 |       '@types/unist': 3.0.3
1551 |       unist-util-is: 6.0.0
1552 |       unist-util-visit-parents: 6.0.1
1553 | 
1554 |   vfile-message@4.0.2:
1555 |     dependencies:
1556 |       '@types/unist': 3.0.3
1557 |       unist-util-stringify-position: 4.0.0
1558 | 
1559 |   vfile@6.0.3:
1560 |     dependencies:
1561 |       '@types/unist': 3.0.3
1562 |       vfile-message: 4.0.2
1563 | 
1564 |   vite@5.4.11:
1565 |     dependencies:
1566 |       esbuild: 0.21.5
1567 |       postcss: 8.4.49
1568 |       rollup: 4.30.1
1569 |     optionalDependencies:
1570 |       fsevents: 2.3.3
1571 | 
1572 |   vitepress@1.5.0(@algolia/client-search@5.19.0)(axios@1.7.9)(postcss@8.4.49)(search-insights@2.17.3):
1573 |     dependencies:
1574 |       '@docsearch/css': 3.8.2
1575 |       '@docsearch/js': 3.8.2(@algolia/client-search@5.19.0)(search-insights@2.17.3)
1576 |       '@iconify-json/simple-icons': 1.2.19
1577 |       '@shikijs/core': 1.26.1
1578 |       '@shikijs/transformers': 1.26.1
1579 |       '@shikijs/types': 1.26.1
1580 |       '@types/markdown-it': 14.1.2
1581 |       '@vitejs/plugin-vue': 5.2.1(vite@5.4.11)(vue@3.5.13)
1582 |       '@vue/devtools-api': 7.7.0
1583 |       '@vue/shared': 3.5.13
1584 |       '@vueuse/core': 11.3.0(vue@3.5.13)
1585 |       '@vueuse/integrations': 11.3.0(axios@1.7.9)(focus-trap@7.6.4)(vue@3.5.13)
1586 |       focus-trap: 7.6.4
1587 |       mark.js: 8.11.1
1588 |       minisearch: 7.1.1
1589 |       shiki: 1.26.1
1590 |       vite: 5.4.11
1591 |       vue: 3.5.13
1592 |     optionalDependencies:
1593 |       postcss: 8.4.49
1594 |     transitivePeerDependencies:
1595 |       - '@algolia/client-search'
1596 |       - '@types/node'
1597 |       - '@types/react'
1598 |       - '@vue/composition-api'
1599 |       - async-validator
1600 |       - axios
1601 |       - change-case
1602 |       - drauu
1603 |       - fuse.js
1604 |       - idb-keyval
1605 |       - jwt-decode
1606 |       - less
1607 |       - lightningcss
1608 |       - nprogress
1609 |       - qrcode
1610 |       - react
1611 |       - react-dom
1612 |       - sass
1613 |       - sass-embedded
1614 |       - search-insights
1615 |       - sortablejs
1616 |       - stylus
1617 |       - sugarss
1618 |       - terser
1619 |       - typescript
1620 |       - universal-cookie
1621 | 
1622 |   vue-demi@0.14.10(vue@3.5.13):
1623 |     dependencies:
1624 |       vue: 3.5.13
1625 | 
1626 |   vue@3.5.13:
1627 |     dependencies:
1628 |       '@vue/compiler-dom': 3.5.13
1629 |       '@vue/compiler-sfc': 3.5.13
1630 |       '@vue/runtime-dom': 3.5.13
1631 |       '@vue/server-renderer': 3.5.13(vue@3.5.13)
1632 |       '@vue/shared': 3.5.13
1633 | 
1634 |   zwitch@2.0.4: {}
1635 | 


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/reference/stdlib/file.md:
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  1 | # File Functions
  2 | 
  3 | - [`basename`](#basename)
  4 | - [`join_paths`](#join-paths) <Badge type="tip" text="v1.2" />
  5 | - [`glob`](#glob)
  6 | - [`size`](#size)
  7 | - [`stdout`](#stdout)
  8 | - [`stderr`](#stderr)
  9 | - [`read_string`](#read-string)
 10 | - [`read_int`](#read-int)
 11 | - [`read_float`](#read-float)
 12 | - [`read_boolean`](#read-boolean)
 13 | - [`read_lines`](#read-lines)
 14 | - [`write_lines`](#write-lines)
 15 | - [`read_tsv`](#read-tsv)
 16 | - [`write_tsv`](#write-tsv)
 17 | - [`read_map`](#read-map)
 18 | - [`write_map`](#write-map)
 19 | - [`read_json`](#read-json)
 20 | - [`write_json`](#write-json)
 21 | - [`read_object`](#read-object)
 22 | - [`read_objects`](#read-objects)
 23 | - [`write_object`](#write-object)
 24 | - [`write_objects`](#write-objects)
 25 | 
 26 | ## `basename`
 27 | 
 28 | Returns the "basename" of a file or directory - the name after the last directory
 29 | separator in the path.
 30 | 
 31 | The optional second parameter specifies a literal suffix to remove from the file name.
 32 | If the file name does not end with the specified suffix then it is ignored.
 33 | 
 34 | **Signatures**
 35 | 
 36 | ```wdl
 37 | String basename(File, [String])
 38 | String basename(Directory, [String])
 39 | ```
 40 | 
 41 | **Parameters**
 42 | 
 43 | 1. **`File|Directory`**: Path of the file or directory to read. If the argument is a
 44 |    `String`, it is assumed to be a local file path relative to the current working
 45 |    directory of the task.
 46 | 2. **`String`**: (Optional) Suffix to remove from the file name.
 47 | 
 48 | **Returns**
 49 | 
 50 | 1.  The file's basename as a `String`.
 51 | 
 52 | **Example**
 53 | 
 54 | ```wdl
 55 | String bn = basename("/path/to/file.txt")
 56 | # `bn` contains `"file.txt"`.
 57 | 
 58 | String bn = basename("/path/to/file.txt", ".txt")
 59 | # `bn` contains `"file"`.
 60 | ```
 61 | 
 62 | ## `join_paths` <Badge type="tip" text="Requires WDL v1.2" />
 63 | 
 64 | Joins together two or more paths into an absolute path in the host filesystem.
 65 | 
 66 | There are three variants of this function:
 67 | 
 68 | 1. `File join_paths(File, String)`: Joins together exactly two paths. The first path may
 69 |    be either absolute or relative and must specify a directory; the second path is
 70 |    relative to the first path and may specify a file or directory.
 71 | 2. `File join_paths(File, Array[String]+)`: Joins together any number of relative paths
 72 |    with a base path. The first argument may be either an absolute or a relative path and
 73 |    must specify a directory. The paths in the second array argument must all be
 74 |    relative. The *last* element may specify a file or directory; all other elements must
 75 |    specify a directory.
 76 | 3. `File join_paths(Array[String]+)`: Joins together any number of paths. The array must
 77 |    not be empty. The *first* element of the array may be either absolute or relative;
 78 |    subsequent path(s) must be relative. The *last* element may specify a file or
 79 |    directory; all other elements must specify a directory.
 80 | 
 81 | An absolute path starts with `/` and indicates that the path is relative to the root of
 82 | the environment in which the task is executed. Only the first path may be absolute. If
 83 | any subsequent paths are absolute, it is an error.
 84 | 
 85 | A relative path does not start with `/` and indicates the path is relative to its parent
 86 | directory. It is up to the execution engine to determine which directory to use as the
 87 | parent when resolving relative paths; by default it is the working directory in which
 88 | the task is executed.
 89 | 
 90 | **Signatures**
 91 | 
 92 | ```wdl
 93 | File join_paths(File, String)
 94 | File join_paths(File, Array[String]+)
 95 | File join_paths(Array[String]+)
 96 | ```
 97 | 
 98 | **Parameters**
 99 | 
100 | 1. **`File|Array[String]+`**: Either a path or an array of paths.
101 | 2. **`String|Array[String]+`**: A relative path or paths; only allowed if the first
102 |    argument is a `File`.
103 | 
104 | **Returns**
105 | 
106 | 1. A `File` representing an absolute path that results from joining all the paths in
107 |    order (left-to-right), and resolving the resulting path against the default parent
108 |    directory if it is relative.
109 | 
110 | **Example**
111 | 
112 | ```wdl
113 | File path = join_paths(["/usr", "bin", "env"])
114 | # `path` points to `/usr/bin/env`.
115 | ```
116 | 
117 | ## `glob`
118 | 
119 | Returns the Bash expansion of the [glob
120 | string](https://en.wikipedia.org/wiki/Glob_(programming)) relative to the task's
121 | execution directory, and in the same order.
122 | 
123 | `glob` finds all of the files (but not the directories) in the same order as would be
124 | matched by running `echo <glob>` in Bash from the task's execution directory.
125 | 
126 | At least in standard Bash, glob expressions are not evaluated recursively, i.e., files
127 | in nested directories are not included.
128 | 
129 | **Signatures**
130 | 
131 | ```wdl
132 | Array[File] glob(String)
133 | ```
134 | 
135 | **Parameters**
136 | 
137 | 1. **`String`**: The glob string.
138 | 
139 | **Returns**
140 | 
141 | 1. An array of all files matched by the glob.
142 | 
143 | **Example**
144 | 
145 | ```wdl
146 | Array<File> paths = glob("*.py")
147 | # `paths` contains all files with the `.py` extension in the current directory.
148 | ```
149 | 
150 | ## `size`
151 | 
152 | Determines the size of a file, directory, or the sum total sizes of the
153 | files/directories contained within a compound value. The files may be optional values;
154 | `None` values have a size of `0.0`. By default, the size is returned in bytes unless the
155 | optional second argument is specified with a [unit](#units-of-storage)
156 | 
157 | In the second variant of the `size` function, the parameter type `X` represents any
158 | compound type that contains `File` or `File?` nested at any depth.
159 | 
160 | If the size cannot be represented in the specified unit because the resulting value is
161 | too large to fit in a `Float`, an error is raised. It is recommended to use a unit that
162 | will always be large enough to handle any expected inputs without numerical overflow.
163 | 
164 | **Signatures**
165 | 
166 | ```wdl
167 | Float size(File|File?, [String])
168 | Float size(Directory|Directory?, [String])
169 | Float size(X|X?, [String])
170 | ```
171 | 
172 | **Parameters**
173 | 
174 | 1. **`File|File?|Directory|Directory?|X|X?`**: A file, directory, or a compound value
175 |    containing files/directories, for which to determine the size.
176 | 2. **`String`**: (Optional) The unit of storage; defaults to 'B'.
177 | 
178 | **Returns**
179 | 
180 | 1. The size of the files/directories as a `Float`.
181 | 
182 | **Example**
183 | 
184 | ```wdl
185 | Float size = size("foo.txt")
186 | # `size` contains the size of `foo.txt`.
187 | ```
188 | 
189 | ## `stdout`
190 | 
191 | Returns the value of the executed command's standard output (stdout) as a `File`. The
192 | engine should give the file a random name and write it in a temporary directory, so as
193 | not to conflict with any other task output files.
194 | 
195 | **Signatures**
196 | 
197 | ```wdl
198 | File stdout()
199 | ```
200 | 
201 | **Parameters**
202 | 
203 | _None._
204 | 
205 | **Returns**
206 | 
207 | 1. A `File` whose contents are the stdout generated by the command of the task where the
208 |    function is called.
209 | 
210 | **Example**
211 | 
212 | ```wdl
213 | String message = read_string(stdout())
214 | # `message` contains the output of the process's `stdout`.
215 | ```
216 | 
217 | ## `stderr`
218 | 
219 | Returns the value of the executed command's standard error (stderr) as a `File`. The
220 | file should be given a random name and written in a temporary directory, so as not to
221 | conflict with any other task output files.
222 | 
223 | 
224 | **Signatures**
225 | 
226 | ```wdl
227 | File stderr()
228 | ```
229 | 
230 | **Parameters**
231 | 
232 | _None._
233 | 
234 | **Returns**
235 | 
236 | 1. A `File` whose contents are the stderr generated by the command of the task where the
237 |    function is called.
238 | 
239 | **Example**
240 | 
241 | ```wdl
242 | String message = read_string(stderr())
243 | # `message` contains the output of the process's `stderr`.
244 | ```
245 | 
246 | ## `read_string`
247 | 
248 | Reads an entire file as a `String`, with any trailing end-of-line characters (`\r` and
249 | `\n`) stripped off. If the file is empty, an empty string is returned.
250 | 
251 | If the file contains any internal newline characters, they are left in tact.
252 | 
253 | **Signatures**
254 | 
255 | ```wdl
256 | String read_string(File)
257 | ```
258 | 
259 | **Parameters**
260 | 
261 | 1. **`File`**: Path of the file to read.
262 | 
263 | **Returns**
264 | 
265 | 1. A `String`.
266 | 
267 | **Example**
268 | 
269 | ```wdl
270 | String message = read_string(stdout())
271 | # `message` contains the output of the process's `stdout`.
272 | ```
273 | 
274 | ## `read_int`
275 | 
276 | Reads a file that contains a single line containing only an integer and (optional)
277 | whitespace. If the line contains a valid integer, that value is returned as an `Int`. If
278 | the file is empty or does not contain a single integer, an error is raised.
279 | 
280 | **Signatures**
281 | 
282 | ```wdl
283 | Int read_int(File)
284 | ```
285 | 
286 | **Parameters**
287 | 
288 | 1. **`File`**: Path of the file to read.
289 | 
290 | **Returns**
291 | 
292 | 1. An `Int`.
293 | 
294 | **Example**
295 | 
296 | ```wdl
297 | Int number = read_int(stdout())
298 | # If `stdout` contains an int, returns the int. Else, an error is raised.
299 | ```
300 | 
301 | ## `read_float`
302 | 
303 | Reads a file that contains only a numeric value and (optional) whitespace. If the line
304 | contains a valid floating point number, that value is returned as a `Float`. If the file
305 | is empty or does not contain a single float, an error is raised.
306 | 
307 | **Signatures**
308 | 
309 | ```wdl
310 | Float read_float(File)
311 | ```
312 | 
313 | **Parameters**
314 | 
315 | 1. **`File`**: Path of the file to read.
316 | 
317 | **Returns**
318 | 
319 | 1. A `Float`.
320 | 
321 | **Example**
322 | 
323 | ```wdl
324 | Float number = read_float(stdout())
325 | # If `stdout` contains a float, returns the float. Else, an error is raised.
326 | ```
327 | 
328 | ## `read_boolean`
329 | 
330 | Reads a file that contains a single line containing only a boolean value and (optional)
331 | whitespace. If the non-whitespace content of the line is "true" or "false", that value
332 | is returned as a `Boolean`. If the file is empty or does not contain a single boolean,
333 | an error is raised. The comparison is case- and whitespace-insensitive.
334 | 
335 | **Signatures**
336 | 
337 | ```wdl
338 | Boolean read_boolean(File)
339 | ```
340 | 
341 | **Parameters**
342 | 
343 | 1. **`File`**: Path of the file to read.
344 | 
345 | **Returns**
346 | 
347 | 1. A `Boolean`.
348 | 
349 | **Example**
350 | 
351 | ```wdl
352 | Boolean value = read_float(stdout())
353 | # If `stdout` contains a boolean, returns the boolean. Else, an error is raised.
354 | ```
355 | 
356 | ## `read_lines`
357 | 
358 | Reads each line of a file as a `String`, and returns all lines in the file as an
359 | `Array[String]`. Trailing end-of-line characters (`\r` and `\n`) are removed from each
360 | line.
361 | 
362 | The order of the lines in the returned `Array[String]` is the order in which the lines
363 | appear in the file.
364 | 
365 | If the file is empty, an empty array is returned.
366 | 
367 | **Signatures**
368 | 
369 | ```wdl
370 | Array[String] read_lines(File)
371 | ```
372 | 
373 | **Parameters**
374 | 
375 | 1. **`File`**: Path of the file to read.
376 | 
377 | **Returns**
378 | 
379 | 1. An `Array[String]` representation of the lines in the file.
380 | 
381 | **Example**
382 | 
383 | ```wdl
384 | Array[String] lines = read_lines("foo.txt")
385 | # `lines` contains the newline-delimited lines read from `foo.txt`.
386 | ```
387 | 
388 | ## `write_lines`
389 | 
390 | Writes a file with one line for each element in a `Array[String]`. All lines are
391 | terminated by the newline (`\n`) character (following the [POSIX
392 | standard](https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_206)).
393 | If the `Array` is empty, an empty file is written.
394 | 
395 | **Signatures**
396 | 
397 | ```wdl
398 | File write_lines(Array[String])
399 | ```
400 | 
401 | **Parameters**
402 | 
403 | 1. **`Array[String]`**: Array of strings to write.
404 | 
405 | **Returns**
406 | 
407 | 1. A `File`.
408 | 
409 | **Example**
410 | 
411 | ```wdl
412 | Array[String] lines = ["first", "second", "third"]
413 | 
414 | File result = write_lines(lines)
415 | # `result` now points to a file with the contents `"first\nsecond\nthird"`.
416 | ```
417 | 
418 | ## `read_tsv`
419 | 
420 | Reads a tab-separated value (TSV) file as an `Array[Array[String]]` representing a table
421 | of values. Trailing end-of-line characters (`\r` and `\n`) are removed from each line.
422 | 
423 | This function has three variants:
424 | 
425 | 1. `Array[Array[String]] read_tsv(File, [false])`: Returns each row of the table as an
426 |    `Array[String]`. There is no requirement that the rows of the table are all the same
427 |    length.
428 | 2. `Array[Object] read_tsv(File, true)`: The second parameter must be `true` and
429 |    specifies that the TSV file contains a header line. Each row is returned as an
430 |    `Object` with its keys determined by the header (the first line in the file) and its
431 |    values as `String`s. All rows in the file must be the same length and the field names
432 |    in the header row must be valid `Object` field names, or an error is raised.
433 | 3. `Array[Object] read_tsv(File, Boolean, Array[String])`: The second parameter
434 |    specifies whether the TSV file contains a header line, and the third parameter is an
435 |    array of field names that is used to specify the field names to use for the returned
436 |    `Object`s. If the second parameter is `true`, the specified field names override
437 |    those in the file's header (i.e., the header line is ignored).
438 | 
439 | If the file is empty, an empty array is returned.
440 | 
441 | If the entire contents of the file can not be read for any reason, the calling task or
442 | workflow fails with an error. Examples of failure include, but are not limited to, not
443 | having access to the file, resource limitations (e.g. memory) when reading the file, and
444 | implementation-imposed file size limits.
445 | 
446 | **Signatures**
447 | 
448 | ```wdl
449 | Array[Array[String]] read_tsv(File)
450 | Array[Object] read_tsv(File, true)
451 | Array[Object] read_tsv(File, Boolean, Array[String])
452 | ```
453 | 
454 | **Parameters**
455 | 
456 | 1. **`File`**: The TSV file to read.
457 | 2. **`Boolean`**: (Optional) Whether to treat the file's first line as a header.
458 | 3. **`Array[String]`**: (Optional) An array of field names. If specified, then the
459 |    second parameter is also required.
460 | 
461 | **Returns**
462 | 
463 | 1. An `Array` of rows in the TSV file, where each row is an `Array[String]` of fields or
464 |    an `Object` with keys determined by the second and third parameters and `String`
465 |    values.
466 | 
467 | **Example**
468 | 
469 | ```wdl
470 | Array[Object] objects = read_tsv("data.tsv", true)
471 | # `objects` holds an array of objects read in from `data.tsv`.
472 | ```
473 | 
474 | ## `write_tsv`
475 | 
476 | Given an `Array` of elements, writes a tab-separated value (TSV) file with one line for
477 | each element.
478 | 
479 | There are three variants of this function:
480 | 
481 | 1. `File write_tsv(Array[Array[String]])`: Each element is concatenated using a tab
482 |    ('\t') delimiter and written as a row in the file. There is no header row.
483 | 
484 | 2. `File write_tsv(Array[Array[String]], true, Array[String])`: The second argument must
485 |    be `true` and the third argument provides an `Array` of column names. The column
486 |    names are concatenated to create a header that is written as the first row of the
487 |    file. All elements must be the same length as the header array.
488 | 
489 | 3. `File write_tsv(Array[Struct], [Boolean, [Array[String]]])`: Each element is a struct
490 |    whose field values are concatenated in the order the fields are defined. The optional
491 |    second argument specifies whether to write a header row. If it is `true`, then the
492 |    header is created from the struct field names. If the second argument is `true`, then
493 |    the optional third argument may be used to specify column names to use instead of the
494 |    struct field names.
495 | 
496 | Each line is terminated by the newline (`\n`) character.
497 | 
498 | The generated file should be given a random name and written in a temporary directory,
499 | so as not to conflict with any other task output files.
500 | 
501 | If the entire contents of the file can not be written for any reason, the calling task
502 | or workflow fails with an error. Examples of failure include, but are not limited to,
503 | insufficient disk space to write the file.
504 | 
505 | **Signatures**
506 | 
507 | ```wdl
508 | File write_tsv(Array[Array[String]]|Array[Struct])
509 | File write_tsv(Array[Array[String]], true, Array[String])
510 | File write_tsv(Array[Struct], Boolean, Array[String])
511 | ```
512 | 
513 | **Parameters**
514 | 
515 | 1. **`Array[Array[String]] | Array[Struct]`**: An array of rows, where each row is either an
516 |    `Array` of column values or a struct whose values are the column values.
517 | 2. **`Boolean`**: (Optional) Whether to write a header row.
518 | 3. **`Array[String]`**: An array of column names. If the first argument is
519 |    `Array[Array[String]]` and the second argument is `true` then it is required,
520 |    otherwise it is optional. Ignored if the second argument is `false`.
521 | 
522 | **Returns**
523 | 
524 | 1. A `File`.
525 | 
526 | **Example**
527 | 
528 | ```wdl
529 | Array[Array[String]] array = [["one", "two", "three"], ["un", "deux", "trois"]]
530 | File result = write_tsv(array)
531 | # `result` points to a file with the content of `array` written as a TSV.
532 | ```
533 | 
534 | ## `read_map`
535 | 
536 | Reads a tab-separated value (TSV) file representing a set of pairs. Each row must have
537 | exactly two columns, e.g., `col1\tcol2`. Trailing end-of-line characters (`\r` and `\n`)
538 | are removed from each line.
539 | 
540 | Each pair is added to a `Map[String, String]` in order. The values in the first column
541 | must be unique; if there are any duplicate keys, an error is raised.
542 | 
543 | If the file is empty, an empty map is returned.
544 | 
545 | **Signatures**
546 | 
547 | ```wdl
548 | Map[String, String] read_map(File)
549 | ```
550 | 
551 | **Parameters**
552 | 
553 | 1. **`File`**: Path of the two-column TSV file to read.
554 | 
555 | **Returns**
556 | 
557 | 1. A `Map[String, String]`, with one element for each row in the TSV file.
558 | 
559 | **Example**
560 | 
561 | ```wdl
562 | Map[String, String] result = read_map(stdout())
563 | # `result` contains a map of the values within the two column tab-delimited text
564 | # returned in `stdout`.
565 | ```
566 | 
567 | ## `write_map`
568 | 
569 | Writes a tab-separated value (TSV) file with one line for each element in a `Map[String,
570 | String]`. Each element is concatenated into a single tab-delimited string of the format
571 | `~{key}\t~{value}`. Each line is terminated by the newline (`\n`) character. If the
572 | `Map` is empty, an empty file is written.
573 | 
574 | Since `Map`s are ordered, the order of the lines in the file is guaranteed to be the
575 | same order that the elements were added to the `Map`.
576 | 
577 | **Signatures**
578 | 
579 | ```wdl
580 | File write_map(Map[String, String])
581 | ```
582 | 
583 | **Parameters**
584 | 
585 | 1. **`Map[String, String]`**: A `Map`, where each element will be a row in the generated
586 |    file.
587 | 
588 | **Returns**
589 | 
590 | 1. A `File`.
591 | 
592 | **Example**
593 | 
594 | ```wdl
595 | Map[String, String] map = {"key1": "value1", "key2": "value2"}
596 | File result = write_map(map)
597 | # `result` points to a file with the contents `"key1\tvalue1\nkey2\tvalue2"`.
598 | ```
599 | 
600 | ## `read_json`
601 | 
602 | Reads a JSON file into a WDL value whose type depends on the file's contents. The
603 | mapping of JSON type to WDL type is:
604 | 
605 | | JSON Type | WDL Type         |
606 | | --------- | ---------------- |
607 | | object    | `Object`         |
608 | | array     | `Array[X]`       |
609 | | number    | `Int` or `Float` |
610 | | string    | `String`         |
611 | | boolean   | `Boolean`        |
612 | | null      | `None`           |
613 | 
614 | The return value is of type [`Union`](#union-hidden-type) and must be used in a context
615 | where it can be coerced to the expected type, or an error is raised. For example, if the
616 | JSON file contains `null`, then the return value will be `None`, meaning the value can
617 | only be used in a context where an optional type is expected.
618 | 
619 | If the JSON file contains an array, then all the elements of the array must be coercible
620 | to the same type, or an error is raised.
621 | 
622 | The `read_json` function does not have access to any WDL type information, so it cannot
623 | return an instance of a specific `Struct` type. Instead, it returns a generic `Object`
624 | value that must be coerced to the desired `Struct` type.
625 | 
626 | Note that an empty file is not valid according to the JSON specification, and so calling
627 | `read_json` on an empty file raises an error.
628 | 
629 | **Signatures**
630 | 
631 | ```wdl
632 | Union read_json(File)
633 | ```
634 | 
635 | **Parameters**
636 | 
637 | 1. **`File`**: Path of the JSON file to read.
638 | 
639 | **Returns**
640 | 
641 | 1. A value whose type is dependent on the contents of the JSON file.
642 | 
643 | **Example**
644 | 
645 | ```wdl
646 | struct Person {
647 |   String name
648 |   Int age
649 | }
650 | 
651 | Person person = read_json(json_file)
652 | # `person` contains a person deserialized from a file.
653 | ```
654 | 
655 | ## `write_json`
656 | 
657 | Writes a JSON file with the serialized form of a WDL value. The following WDL types can
658 | be serialized:
659 | 
660 | | WDL Type         | JSON Type |
661 | | ---------------- | --------- |
662 | | `Struct`         | object    |
663 | | `Object`         | object    |
664 | | `Map[String, X]` | object    |
665 | | `Array[X]`       | array     |
666 | | `Int`            | number    |
667 | | `Float`          | number    |
668 | | `String`         | string    |
669 | | `File`           | string    |
670 | | `Boolean`        | boolean   |
671 | | `None`           | null      |
672 | 
673 | When serializing compound types, all nested types must be serializable or an error is
674 | raised.
675 | 
676 | **Signatures**
677 | 
678 | ```wdl
679 | File write_json(X)
680 | ```
681 | 
682 | **Parameters**
683 | 
684 | 1. **`X`**: A WDL value of a supported type.
685 | 
686 | **Returns**
687 | 
688 | 1. A `File`.
689 | 
690 | **Example**
691 | 
692 | ```wdl
693 | struct Person {
694 |     String name
695 |     Int age
696 | }
697 | 
698 | Array[Person] people = [
699 |     Person {
700 |          name: "Jane Doe",
701 |          age: 29,
702 |     },
703 |     Person {
704 |          name: "John Doe",
705 |          age: 28,
706 |     }
707 | ]
708 | 
709 | File result = write_tsv(people)
710 | # `people` points to a file with the contents `"Jane Doe\t29\nJohn Doe\t28"`.
711 | ```
712 | 
713 | ## `read_object`
714 | 
715 | Reads a tab-separated value (TSV) file representing the names and values of the members
716 | of an `Object`. There must be exactly two rows, and each row must have the same number
717 | of elements, otherwise an error is raised. Trailing end-of-line characters (`\r` and
718 | `\n`) are removed from each line.
719 | 
720 | The first row specifies the object member names. The names in the first row must be
721 | unique; if there are any duplicate names, an error is raised.
722 | 
723 | The second row specifies the object member values corresponding to the names in the
724 | first row. All of the `Object`'s values are of type `String`.
725 | 
726 | **Signatures**
727 | 
728 | ```wdl
729 | Object read_object(File)
730 | ```
731 | 
732 | **Parameters**
733 | 
734 | 1. **`File`**: Path of the two-row TSV file to read.
735 | 
736 | **Returns**
737 | 
738 | 1. An `Object`, with as many members as there are unique names in the TSV.
739 | 
740 | **Example**
741 | 
742 | ```wdl
743 | Object object  = read_object(stdout())
744 | # `object` contains an `Object` with the key value pairs from `stdout`.
745 | ```
746 | 
747 | ## `read_objects`
748 | 
749 | Reads a tab-separated value (TSV) file representing the names and values of the members
750 | of any number of `Object`s. Trailing end-of-line characters (`\r` and `\n`) are removed
751 | from each line.
752 | 
753 | The first line of the file must be a header row with the names of the object members.
754 | The names in the first row must be unique; if there are any duplicate names, an error is
755 | raised.
756 | 
757 | There are any number of additional rows, where each additional row contains the values
758 | of an object corresponding to the member names. Each row in the file must have the same
759 | number of fields as the header row. All of the `Object`'s values are of type `String`.
760 | 
761 | If the file is empty or contains only a header line, an empty array is returned.
762 | 
763 | **Signatures**
764 | 
765 | ```wdl
766 | Array[Object] read_objects(File)
767 | ```
768 | 
769 | **Parameters**
770 | 
771 | 1. **`File`**: Path of the TSV file to read.
772 | 
773 | **Returns**
774 | 
775 | 1. An `Array[Object]`, with `N-1` elements, where `N` is the number of rows in the file.
776 | 
777 | **Example**
778 | 
779 | ```wdl
780 | Array[Object] objects = read_objects(stdout())
781 | # `objects` contains an array of `Object`s with the key value pairs provided on each
782 | # line from `stdout`.
783 | ```
784 | 
785 | ## `write_object`
786 | 
787 | Writes a tab-separated value (TSV) file with the contents of a `Object` or `Struct`. The
788 | file contains two tab-delimited lines. The first line is the names of the members, and
789 | the second line is the corresponding values. Each line is terminated by the newline
790 | (`\n`) character. The ordering of the columns is unspecified.
791 | 
792 | The member values must be serializable to strings, meaning that only primitive types are
793 | supported. Attempting to write a `Struct` or `Object` that has a compound member value
794 | results in an error.
795 | 
796 | **Signatures**
797 | 
798 | ```wdl
799 | File write_object(Struct|Object)
800 | ```
801 | 
802 | **Parameters**
803 | 
804 | 1. **`Struct|Object`**: An object to write.
805 | 
806 | **Returns**
807 | 
808 | 1. A `File`.
809 | 
810 | **Example**
811 | 
812 | ```wdl
813 | struct Person {
814 |     String name
815 |     Int age
816 | }
817 | 
818 | Person person = Person {
819 |     name: "Jane Doe",
820 |     age: 29,
821 | }
822 | 
823 | File result = write_object(person)
824 | # `result` points to a file that contains the contents `"name\tage\nJane Doe\t29"`.
825 | ```
826 | 
827 | ## `write_objects`
828 | 
829 | Writes a tab-separated value (TSV) file with the contents of a `Array[Struct]` or
830 | `Array[Object]`. All elements of the `Array` must have the same member names, or an
831 | error is raised.
832 | 
833 | The file contains `N+1` tab-delimited lines, where `N` is the number of elements in the
834 | `Array`. The first line is the names of the `Struct`/`Object` members, and the
835 | subsequent lines are the corresponding values for each element. Each line is terminated
836 | by a newline (`\n`) character. The lines are written in the same order as the elements
837 | in the `Array`. The ordering of the columns is the same as the order in which the
838 | `Struct`'s members are defined; the column ordering for `Object`s is unspecified. If the
839 | `Array` is empty, an empty file is written.
840 | 
841 | The member values must be serializable to strings, meaning that only primitive types are
842 | supported. Attempting to write a `Struct` or `Object` that has a compound member value
843 | results in an error.
844 | 
845 | **Signatures**
846 | 
847 | ```wdl
848 | File write_objects(Array[Struct|Object])
849 | ```
850 | 
851 | **Parameters**
852 | 
853 | 1. **`Array[Struct|Object]`**: An array of objects to write.
854 | 
855 | **Returns**
856 | 
857 | 1. A `File`.
858 | 
859 | **Example**
860 | 
861 | ```wdl
862 | struct Person {
863 |     String name
864 |     Int age
865 | }
866 | 
867 | Array[Person] people = [
868 |     Person {
869 |         name: "Jane Doe",
870 |         age: 29,
871 |     },
872 |     Person {
873 |         name: "John Doe",
874 |         age: 28,
875 |     }
876 | ]
877 | 
878 | File result = write_objects(people)
879 | # `result` points to a file that contains the contents
880 | # `"name\tage\nJane Doe\t29\nJohn Doe\t28"`.
881 | ```
882 | 


--------------------------------------------------------------------------------
/reference/stdlib/numeric.md:
--------------------------------------------------------------------------------
  1 | # Numeric Functions
  2 | 
  3 | - [`floor`](#floor)
  4 | - [`ceil`](#ceil)
  5 | - [`round`](#round)
  6 | - [`min`](#min)
  7 | - [`max`](#max)
  8 | 
  9 | ## `floor`
 10 | 
 11 | Rounds a floating point number **down** to the next lowest integer.
 12 | 
 13 | **Signatures**
 14 | 
 15 | ```wdl
 16 | Int floor(Float)
 17 | ```
 18 | 
 19 | **Parameters**
 20 | 
 21 | 1. **`Float`**: the number to round.
 22 | 
 23 | **Returns**
 24 | 
 25 | 1. An integer.
 26 | 
 27 | **Example**
 28 | 
 29 | ```wdl
 30 | Int three = floor(3.14)
 31 | # `three` now contains `3`.
 32 | ```
 33 | 
 34 | ## `ceil`
 35 | 
 36 | Rounds a floating point number **up** to the next highest integer.
 37 | 
 38 | **Signatures**
 39 | 
 40 | ```wdl
 41 | Int ceil(Float)
 42 | ```
 43 | 
 44 | **Parameters**
 45 | 
 46 | 1. **`Float`**: the number to round.
 47 | 
 48 | **Returns**
 49 | 
 50 | 1. An integer.
 51 | 
 52 | **Example**
 53 | 
 54 | ```wdl
 55 | Int four = ceil(3.14)
 56 | # `four` now contains `4`.
 57 | ```
 58 | 
 59 | ## `round`
 60 | 
 61 | Rounds a floating point number to the nearest integer based on standard rounding rules
 62 | ("round half up").
 63 | 
 64 | **Signatures**
 65 | 
 66 | ```wdl
 67 | Int round(Float)
 68 | ```
 69 | 
 70 | **Parameters**
 71 | 
 72 | 1. **`Float`**: the number to round.
 73 | 
 74 | **Returns**
 75 | 
 76 | 1. An integer.
 77 | 
 78 | **Example**
 79 | 
 80 | ```wdl
 81 | Int three = round(3.14)
 82 | # `three` now contains `3`.
 83 | ```
 84 | 
 85 | ## `min`
 86 | 
 87 | Returns the smaller of two values. If both values are `Int`s, the return value is an
 88 | `Int`, otherwise it is a `Float`.
 89 | 
 90 | **Signatures**
 91 | 
 92 | ```wdl
 93 | Int min(Int, Int)
 94 | Float min(Int, Float)
 95 | Float min(Float, Int)
 96 | Float min(Float, Float)
 97 | ```
 98 | 
 99 | **Parameters**
100 | 
101 | 1. **`Int|Float`**: the first number to compare.
102 | 2. **`Int|Float`**: the second number to compare.
103 | 
104 | **Returns**
105 | 
106 | 1. The smaller of the two arguments.
107 | 
108 | **Example**
109 | 
110 | ```wdl
111 | Int value1
112 | Float value2
113 | 
114 | Float result = min(value1, value2)
115 | # This is equivalent to `if value1 < value2 then value1 else value2`.
116 | ```
117 | 
118 | ## `max`
119 | 
120 | Returns the larger of two values. If both values are `Int`s, the return value is an
121 | `Int`, otherwise it is a `Float`.
122 | 
123 | **Signatures**
124 | 
125 | ```wdl
126 | Int max(Int, Int)
127 | Float max(Int, Float)
128 | Float max(Float, Int)
129 | Float max(Float, Float)
130 | ```
131 | 
132 | **Parameters**
133 | 
134 | 1. **`Int|Float`**: the first number to compare.
135 | 2. **`Int|Float`**: the second number to compare.
136 | 
137 | **Returns**
138 | 
139 | 1. The larger of the two arguments.
140 | 
141 | **Example**
142 | 
143 | ```wdl
144 | Int value1
145 | Float value2
146 | 
147 | Float result = max(value1, value2)
148 | # This is equivalent to `if value1 > value2 then value1 else value2`.
149 | ```
150 | 


--------------------------------------------------------------------------------
/reference/stdlib/string-array.md:
--------------------------------------------------------------------------------
  1 | # String Array Functions
  2 | 
  3 | - [`prefix`](#prefix)
  4 | - [`suffix`](#suffix)
  5 | - [`quote`](#quote)
  6 | - [`squote`](#squote)
  7 | - [`sep`](#sep)
  8 | 
  9 | ## `prefix`
 10 | 
 11 | Adds a prefix to each element of the input array of primitive values. Equivalent to
 12 | evaluating `"~{prefix}~{array[i]}"` for each `i` in `range(length(array))`.
 13 | 
 14 | **Signatures**
 15 | 
 16 | ```wdl
 17 | Array[String] prefix(String, Array[P])
 18 | ```
 19 | 
 20 | **Parameters**
 21 | 
 22 | 1. **`String`**: The prefix to prepend to each element in the array.
 23 | 2. **`Array[P]`**: Array with a primitive element type.
 24 | 
 25 | **Returns**
 26 | 
 27 | 1. An `Array[String]` with the prefixed elements of the input array.
 28 | 
 29 | **Example**
 30 | 
 31 | ```wdl
 32 | Array[String] names = ["John", "Jane", "world"]
 33 | String greetings = prefix("Hello, ", names)
 34 | # `greetings` now contains `["Hello, John", "Hello, Jane", "Hello, world"]`.
 35 | ```
 36 | 
 37 | ## `suffix`
 38 | 
 39 | Adds a suffix to each element of the input array of primitive values. Equivalent to
 40 | evaluating `"~{array[i]}~{suffix}"` for each `i` in `range(length(array))`.
 41 | 
 42 | **Signatures**
 43 | 
 44 | ```wdl
 45 | Array[String] suffix(String, Array[P])
 46 | ```
 47 | 
 48 | **Parameters**
 49 | 
 50 | 1. **`String`**: The suffix to append to each element in the array.
 51 | 2. **`Array[P]`**: Array with a primitive element type.
 52 | 
 53 | **Returns**
 54 | 
 55 | 1. An `Array[String]` the suffixed elements of the input array.
 56 | 
 57 | **Example**
 58 | 
 59 | ```wdl
 60 | Array[String] names = ["John", "Jane"]
 61 | String responses = suffix(" says 'hi!'", names)
 62 | # `responses` now contains `["John says 'hi!'", "Jane says 'hi!'"]`.
 63 | ```
 64 | 
 65 | ## `quote`
 66 | 
 67 | Adds double-quotes (`"`) around each element of the input array of primitive values.
 68 | Equivalent to evaluating `'"~{array[i]}"'` for each `i` in `range(length(array))`.
 69 | 
 70 | **Signatures**
 71 | 
 72 | ```wdl
 73 | Array[String] quote(Array[P])
 74 | ```
 75 | 
 76 | **Parameters**
 77 | 
 78 | 1. **`Array[P]`**: Array with a primitive element type.
 79 | 
 80 | **Returns**
 81 | 
 82 | 1. An `Array[String]` the double-quoted elements of the input array.
 83 | 
 84 | **Example**
 85 | 
 86 | ```wdl
 87 | Array[String] numbers = [1, 2, 3]
 88 | String quoted = quote(numbers)
 89 | # `quoted` now contains `["\"1\"", "\"2\"", "\"3\""]`.
 90 | ```
 91 | 
 92 | ## `squote`
 93 | 
 94 | Adds single-quotes (`'`) around each element of the input array of primitive values.
 95 | Equivalent to evaluating `"'~{array[i]}'"` for each `i` in `range(length(array))`.
 96 | 
 97 | **Signatures**
 98 | 
 99 | ```wdl
100 | Array[String] squote(Array[P])
101 | ```
102 | 
103 | **Parameters**
104 | 
105 | 1. **`Array[P]`**: Array with a primitive element type.
106 | 
107 | **Returns**
108 | 
109 | 1. An `Array[String]` the single-quoted elements of the input array.
110 | 
111 | **Example**
112 | 
113 | ```wdl
114 | Array[String] numbers = [1, 2, 3]
115 | String quoted = squote(numbers)
116 | # `quoted` now contains `["'1'", "'2'", "'3'"]`.
117 | ```
118 | 
119 | ## `sep`
120 | 
121 | Concatenates the elements of an array together into a string with the given separator
122 | between consecutive elements. There are always `N-1` separators in the output string,
123 | where `N` is the length of the input array. A separator is never added after the last
124 | element. Returns an empty string if the array is empty.
125 | 
126 | **Signatures**
127 | 
128 | ```wdl
129 | String sep(String, Array[P])
130 | ```
131 | 
132 | **Parameters**
133 | 
134 | 1. `String`: Separator string. 
135 | 2. `Array[P]`: Array of strings to concatenate.
136 | 
137 | **Returns**
138 | 
139 | 1. A `String` with the concatenated elements of the array delimited by the separator
140 |    string.
141 | 
142 | **Example**
143 | 
144 | ```wdl
145 | Array[String] letters = ["a", "b", "c", "d"]
146 | String letters_with_commas = sep(", ", letters)
147 | # `letters_with_commas` now contains `"a, b, c, d"`.
148 | ```
149 | 


--------------------------------------------------------------------------------
/reference/stdlib/string.md:
--------------------------------------------------------------------------------
  1 | # String Functions
  2 | 
  3 | - [`find`](#find) <Badge type="tip" text="v1.2" />
  4 | - [`matches`](#matches) <Badge type="tip" text="v1.2" />
  5 | - [`sub`](#sub)
  6 | 
  7 | ## `find` <Badge type="tip" text="Requires WDL v1.2" />
  8 | 
  9 | Given two `String` parameters `input` and `pattern`, searches for the occurrence of
 10 | `pattern` within `input` and returns the first match or `None` if there are no matches.
 11 | `pattern` is a [regular expression](https://en.wikipedia.org/wiki/Regular_expression)
 12 | and is evaluated as a [POSIX Extended Regular Expression
 13 | (ERE)](https://en.wikipedia.org/wiki/Regular_expression#POSIX_basic_and_extended).
 14 | 
 15 | 
 16 | Note that regular expressions are written using regular WDL strings, so backslash
 17 | characters need to be double-escaped. For example:
 18 | 
 19 | ```wdl
 20 | String? first_match = find("hello\tBob", "\\t")
 21 | ```
 22 | 
 23 | **Signatures**
 24 | 
 25 | ```wdl
 26 | String? find(String, String)
 27 | ```
 28 | 
 29 | **Parameters**
 30 | 
 31 | 1. **`String`**: the input string to search.
 32 | 2. **`String`**: the pattern to search for.
 33 | 
 34 | **Returns**
 35 | 
 36 | 1. The contents of the first match, or `None` if `pattern` does not match `input`.
 37 | 
 38 | **Example**
 39 | 
 40 | ```wdl
 41 | String? match = find("Hello, world!", "e..o");
 42 | # `match` now contains `ello`.
 43 | ```
 44 | 
 45 | ## `matches` <Badge type="tip" text="Requires WDL v1.2" />
 46 | 
 47 | Given two `String` parameters `input` and `pattern`, tests whether `pattern` matches
 48 | `input` at least once. `pattern` is a [regular
 49 | expression](https://en.wikipedia.org/wiki/Regular_expression) and is evaluated as a
 50 | [POSIX Extended Regular Expression
 51 | (ERE)](https://en.wikipedia.org/wiki/Regular_expression#POSIX_basic_and_extended).
 52 | 
 53 | To test whether `pattern` matches the entire `input`, make sure to begin and end the
 54 | pattern with anchors. For example:
 55 | 
 56 | ```wdl
 57 | Boolean full_match = matches("abc123", "^a.+3$")
 58 | ```
 59 | 
 60 | Note that regular expressions are written using regular WDL strings, so backslash
 61 | characters need to be double-escaped. For example:
 62 | 
 63 | ```wdl
 64 | Boolean has_tab = matches("hello\tBob", "\\t")
 65 | ```
 66 | 
 67 | **Signatures**
 68 | 
 69 | ```wdl
 70 | Boolean matches(String, String)
 71 | ```
 72 | 
 73 | **Parameters**
 74 | 
 75 | 1. **`String`**: the input string to search.
 76 | 2. **`String`**: the pattern to search for.
 77 | 
 78 | **Returns**
 79 | 
 80 | 1. `true` if `pattern` matches `input` at least once, otherwise `false`.
 81 | 
 82 | **Example**
 83 | 
 84 | ```wdl
 85 | Boolean matches = matches("sample1234_R1.fastq", "_R1");
 86 | # `matches` now contains `true`.
 87 | ```
 88 | 
 89 | ## `sub`
 90 | 
 91 | Given three String parameters `input`, `pattern`, `replace`, this function replaces all
 92 | non-overlapping occurrences of `pattern` in `input` by `replace`. `pattern` is a
 93 | [regular expression](https://en.wikipedia.org/wiki/Regular_expression) and is evaluated
 94 | as a [POSIX Extended Regular Expression
 95 | (ERE)](https://en.wikipedia.org/wiki/Regular_expression#POSIX_basic_and_extended).
 96 | Regular expressions are written using regular WDL strings, so backslash characters need
 97 | to be double-escaped (e.g., `"\\t"`).
 98 | 
 99 | 
100 | **Signatures**
101 | 
102 | ```wdl
103 | String sub(String, String, String)
104 | ```
105 | 
106 | **Parameters**
107 | 
108 | 1. **`String`**: the input string.
109 | 2. **`String`**: the pattern to search for.
110 | 3. **`String`**: the replacement string.
111 | 
112 | **Returns**
113 | 
114 | 1. the input string, with all occurrences of the pattern replaced by the replacement
115 |    string.
116 | 
117 | **Example**
118 | 
119 | ```wdl
120 | String chocolike = "I like chocolate when\nit's late"
121 | String chocolove = sub(chocolike, "like", "love") #
122 | 
123 | # `chocolove` now contains `"I love chocolate when\nit's late"`.
124 | ```
125 | 


--------------------------------------------------------------------------------
/reference/upgrade-guide.md:
--------------------------------------------------------------------------------
  1 | ---
  2 | outline: [1, 2]
  3 | ---
  4 | 
  5 | # Overview
  6 | 
  7 | The Workflow Description Language has a number of **versions** that are
  8 | constantly improving. This guide lists all major versions of the language—the
  9 | major improvements for each version, common pitfalls when upgrading, and how to
 10 | get help.
 11 | 
 12 | If you're interested in learning more about how versioning works and how you can
 13 | specify the version of your WDL documents, see the [Versioning section] within
 14 | the Language Guide.
 15 | 
 16 | ::: tip
 17 | Changes are grouped in terms of their **impact**. The word "impact" here is a
 18 | combination of "how important is the change" along with "how many existing WDL
 19 | documents are likely to be affected by this change". They are subjective
 20 | determinations made by the upgrade guide curator during the curator process, but
 21 | they are often helpful in quickly scanning upgrade elements to see which might
 22 | apply to your situation.
 23 | :::
 24 | 
 25 | # WDL v1.2
 26 | 
 27 | WDL v1.2 introduces a great deal of new syntax and changes to the specification.
 28 | Notably, changes were backwards compatible with all previous `v1.x` releases.
 29 | This sections only covers the high points related to upgrading—the full release
 30 | notes can be found [here][wdl-v1.2-release-notes].
 31 | 
 32 | ### Checklist
 33 | 
 34 | Use this checklist to ensure you hit all of the sections.
 35 | 
 36 | #### Moderate impact changes 
 37 | 
 38 | <input type="checkbox" /> New `Directory` type ([link](#new-directory-type)).<br />
 39 | <input type="checkbox" /> Replacement of `runtime` section with `requirements` and `hints` sections ([link](#replacement-of-runtime-with-requirements-and-hints)). <br />
 40 | <input type="checkbox" /> Deprecation of `runtime` section ([link](#deprecation-of-runtime-section)). <br />
 41 | <input type="checkbox" /> New standard library functions
 42 | ([link](#new-standard-library-functions)). <br />
 43 | <input type="checkbox" /> Multi-line strings ([link](#multi-line-strings)). <br />
 44 | <input type="checkbox" /> Optional `input:` statement ([link](#optional-input-statement)). <br />
 45 | 
 46 | #### Low impact changes 
 47 | 
 48 | <input type="checkbox" /> Addition of workflow `hints` ([link](#addition-of-workflow-hints)). <br />
 49 | <input type="checkbox" /> New requirements and hints keys ([link](#new-requirements-and-hints-keys)). <br />
 50 | <input type="checkbox" /> Metadata sections for structs ([link](#metadata-sections-for-structs)). <br />
 51 | <input type="checkbox" /> Exponentiation operator ([link](#exponentiation-operator)). <br />
 52 | 
 53 | ## Moderate impact changes
 54 | 
 55 | ### New `Directory` type
 56 | 
 57 | The `Directory` type was introduced in
 58 | [#641](https://github.com/openwdl/wdl/pull/641) to better semantically indicate
 59 | the use of a directory. If the intention of any of your arguments is to be used
 60 | to refer to a directory on the filesystem, you are encouraged to update the
 61 | parameters to a `Directory` type.
 62 | 
 63 | ### Deprecation of `runtime` section
 64 | 
 65 | The `runtime` section, which previously held both requirement constraints and
 66 | hints to the execution engine, has now been split into the `requirements`
 67 | ([#540](https://github.com/openwdl/wdl/issues/540)) section and `hints`
 68 | ([#541](https://github.com/openwdl/wdl/issues/541)) section respectively. You
 69 | should split out these keys based on the definitions in the
 70 | specification<sup>[1](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-requirements-section),
 71 | [2](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-hints-section)</sup>.
 72 | 
 73 | 🗑️ This change deprecates the `runtime` section, which will be removed in WDL v2.0.
 74 | That being said, if desired, you can continue to use the `runtime` section in your WDL
 75 | documents—it's just not recommended.
 76 | 
 77 | ### New standard library functions
 78 | 
 79 | The following are new standard library functions and their definitions. You are
 80 | encouraged to read through them and replace any custom functionality that would
 81 | now be duplicated in favor of these functions.
 82 | 
 83 | - `contains_key`: whether or not a `Map` or `Object` contain a specific member
 84 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-contains_key)).
 85 | - `values`: get the values from a `Map`
 86 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-values)).
 87 | - `find`: search for a regular expression in a string
 88 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-find)).
 89 | - `matches`: whether a string match a regular expression
 90 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-matches)).
 91 | - `chunk`: split an array into sub-arrays
 92 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-chunk)).
 93 | - `join_paths`: join two or more paths
 94 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-join_paths)).
 95 | - `contains`: whether an array contains a specified value
 96 |   ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-contains)).
 97 | 
 98 | 
 99 | ### Multi-line strings
100 | 
101 | Multi-line strings were introduced with the following syntax.
102 | 
103 | ```wdl
104 | String foo = <<<
105 |   my
106 |   multi-line
107 |   string
108 | >>>
109 | ```
110 | 
111 | ### Optional `input:` statement
112 | 
113 | As noted in [#524](https://github.com/openwdl/wdl/pull/524), the `input:`
114 | statement that precedes call bodies is unnecessary historical boilerplate. This
115 | statement is now optional in `call` bodies. You are encouraged to remove these
116 | from your `call` bodies.
117 | 
118 | ## Low impact changes
119 | 
120 | ### Addition of workflow `hints`
121 | 
122 | Workflows gained a `hints` section in
123 | [#543](https://github.com/openwdl/wdl/issues/543). You are encouraged to go read
124 | the supported workflow
125 | hints<sup>[1](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#workflow-hints)</sup>
126 | and apply them to your workflow if any are relevant.
127 | 
128 | ### New requirements and hints keys
129 | 
130 | - The following keys were added to the task `requirements` section: `fpga`
131 | <sup>[1](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#hardware-accelerators-gpu-and--fpga)</sup>.
132 | - The following keys were added to the task `hints` section: `disks`
133 | <sup>[1](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-disks)</sup>,
134 | `gpu`
135 | <sup>[2](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-gpu-and--fpga)</sup>,
136 | and `fpga`
137 | <sup>[2](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#-gpu-and--fpga)</sup>.
138 | 
139 | You are encouraged to examine these keys are determine if any of these should be
140 | specified for your tasks.
141 | 
142 | ### Metadata sections for structs
143 | 
144 | Similarly to tasks and workflows, structs now have `meta` and `parameter_meta`
145 | sections. You are encouraged to use these fields according to the definition in
146 | the
147 | specification<sup>[1](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#struct-definition)</sup>.
148 | 
149 | ### Exponentiation operator
150 | 
151 | The exponentiation operator (`**`) was added in this release. You are encouraged
152 | to go and update any manual exponentiation to use this operator instead.
153 | 
154 | You are encouraged to go read the specification section on this concept
155 | ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md#multi-line-strings))
156 | and use them where appropriate.
157 | 
158 | # Prior WDL versions
159 | 
160 | Versions of WDL prior to the ones outlined in this guide did not exist at the
161 | time the upgrade guide was created. As such, they are not included in the guide.
162 | 
163 | [wdl-v1.2-release-notes]: https://github.com/openwdl/wdl/releases/tag/v1.2.0
164 | [Versioning section]: ../language-guide/versions.md
165 | 


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