From e43e042104b728df1f1ad6e6145945d2b32331a6 Mon Sep 17 00:00:00 2001 From: Peter Huene Date: Mon, 19 Aug 2024 11:08:25 -0700 Subject: [PATCH 01/28] Update GOVERNANCE.md (#681) Add Peter Huene and Mark Schreiber to `GOVERNANCE.md`. --------- Co-authored-by: John Didion --- GOVERNANCE.md | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/GOVERNANCE.md b/GOVERNANCE.md index 1b013066..80799e91 100644 --- a/GOVERNANCE.md +++ b/GOVERNANCE.md @@ -6,19 +6,21 @@ WDL has a community-driven development process where most decisions are made thr Current core team members are: -| Name | Organization | github | -| :-------------------- | :----------------------------------- | :------------------------------------------------ | -| John Didion | Fulcrum Genomics | [jdidion](https://github.com/jdidion) | -| Taylor Firman | Fred Hutch | [tefirman](https://github.com/tefirman) | -| Michael Franklin | Centre for Population Genomics | [illusional](https://github.com/illusional) | -| Jeff Gentry | Fulcrum Genomics | [geoffjentry](https://github.com/geoffjentry) | -| Mike Lin | Chan Zuckerberg Initiative | [mlin](https://github.com/mlin) | -| Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | -| Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | -| Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | -| Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | -| Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | -| Ruben Vorderman | Leiden University Medical Center | [rhpvorderman](https://github.com/rhpvorderman) | +| Name | Organization | github | +| :-------------------- | :------------------------------------ | :------------------------------------------------ | +| John Didion | Fulcrum Genomics | [jdidion](https://github.com/jdidion) | +| Taylor Firman | Fred Hutch | [tefirman](https://github.com/tefirman) | +| Michael Franklin | Centre for Population Genomics | [illusional](https://github.com/illusional) | +| Jeff Gentry | Fulcrum Genomics | [geoffjentry](https://github.com/geoffjentry) | +| Peter Huene | St. Jude Children's Research Hospital | [peterhuene](https://github.com/peterhuene) | +| Mike Lin | Chan Zuckerberg Initiative | [mlin](https://github.com/mlin) | +| Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | +| Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | +| Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | +| Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | +| Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | +| Mark Schreiber | Amazon | [markjschreiber](https://github.com/markjschreiber) | +| Ruben Vorderman | Leiden University Medical Center | [rhpvorderman](https://github.com/rhpvorderman) | At the core group's discretion a new member may be added by a majority vote. This addition will be done to recognize **significant** contributions to the community. *Contributions* include such things as: From 531eded6c68393e64ec12efe4d5c22d787036ffa Mon Sep 17 00:00:00 2001 From: Mark Schreiber Date: Wed, 25 Sep 2024 16:29:12 -0400 Subject: [PATCH 02/28] Update README.md correction - HealthOmics doesn't require installation --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9be70103..d3099fd1 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ Please see the documentation associated with each tool/platform for information | Implementation | Requires Installation | Local Execution | HPC | Cloud | | ------------------------------------------------------------------------------ | --------------------- | --------------- | ----- | --------------------- | -| [AWS HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html) | Yes | No | No | AWS | +| [AWS HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html) | No | No | No | AWS | | [Cromwell](https://github.com/broadinstitute/cromwell) * | Yes | Yes | Many | AWS Batch, Azure, GCP | | [dxCompiler](https://github.com/dnanexus/dxCompiler) | Yes | No | No | DNAnexus | | [MiniWDL](https://github.com/chanzuckerberg/miniwdl) | Yes | Yes | SLURM | AWS Batch | From 439a2bca3a2c9f059566c8f78539fed48f21694b Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Mon, 13 Jan 2025 19:42:16 -0600 Subject: [PATCH 03/28] docs: fix table formatting --- GOVERNANCE.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/GOVERNANCE.md b/GOVERNANCE.md index 80799e91..9f0d76d7 100644 --- a/GOVERNANCE.md +++ b/GOVERNANCE.md @@ -2,25 +2,25 @@ OpenWDL Governance and Process ============================== -WDL has a community-driven development process where most decisions are made through consensus, under the stewardship of a 'core team'. The core team is responsible for steering the design and development process, overseeing the introduction of new features, setting priorities and release schedule, and ultimately making decisions for the rare instances where there is no community consensus. +WDL has a community-driven development process where most decisions are made through consensus, under the stewardship of a 'core team'. The core team is responsible for steering the design and development process, overseeing the introduction of new features, setting priorities and release schedule, and ultimately making decisions for the rare instances where there is no community consensus. Current core team members are: -| Name | Organization | github | -| :-------------------- | :------------------------------------ | :------------------------------------------------ | -| John Didion | Fulcrum Genomics | [jdidion](https://github.com/jdidion) | -| Taylor Firman | Fred Hutch | [tefirman](https://github.com/tefirman) | -| Michael Franklin | Centre for Population Genomics | [illusional](https://github.com/illusional) | -| Jeff Gentry | Fulcrum Genomics | [geoffjentry](https://github.com/geoffjentry) | -| Peter Huene | St. Jude Children's Research Hospital | [peterhuene](https://github.com/peterhuene) | -| Mike Lin | Chan Zuckerberg Initiative | [mlin](https://github.com/mlin) | -| Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | -| Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | -| Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | -| Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | -| Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | -| Mark Schreiber | Amazon | [markjschreiber](https://github.com/markjschreiber) | -| Ruben Vorderman | Leiden University Medical Center | [rhpvorderman](https://github.com/rhpvorderman) | +| Name | Organization | github | +| :-------------------- | :------------------------------------ | :-------------------------------------------------- | +| John Didion | Fulcrum Genomics | [jdidion](https://github.com/jdidion) | +| Taylor Firman | Fred Hutch | [tefirman](https://github.com/tefirman) | +| Michael Franklin | Centre for Population Genomics | [illusional](https://github.com/illusional) | +| Jeff Gentry | Fulcrum Genomics | [geoffjentry](https://github.com/geoffjentry) | +| Peter Huene | St. Jude Children's Research Hospital | [peterhuene](https://github.com/peterhuene) | +| Mike Lin | Chan Zuckerberg Initiative | [mlin](https://github.com/mlin) | +| Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | +| Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | +| Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | +| Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | +| Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | +| Mark Schreiber | Amazon | [markjschreiber](https://github.com/markjschreiber) | +| Ruben Vorderman | Leiden University Medical Center | [rhpvorderman](https://github.com/rhpvorderman) | At the core group's discretion a new member may be added by a majority vote. This addition will be done to recognize **significant** contributions to the community. *Contributions* include such things as: From a0ef626d80d9bf2bcbd2c35d12477824b83ea932 Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Mon, 13 Jan 2025 19:44:08 -0600 Subject: [PATCH 04/28] docs: add `claymcleod` to governance committee --- GOVERNANCE.md | 1 + 1 file changed, 1 insertion(+) diff --git a/GOVERNANCE.md b/GOVERNANCE.md index 9f0d76d7..b2a638d8 100644 --- a/GOVERNANCE.md +++ b/GOVERNANCE.md @@ -17,6 +17,7 @@ Current core team members are: | Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | | Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | | Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | +| Clay McLeod | St. Jude Children's Research Hospital | [claymcleod](https://github.com/claymcleod) | | Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | | Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | | Mark Schreiber | Amazon | [markjschreiber](https://github.com/markjschreiber) | From 585d984ad4c0c3c657d46c9ecb6f9179ab39d149 Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Sat, 16 Nov 2024 11:35:46 -0600 Subject: [PATCH 05/28] docs: updates the `README.md` content This commit is the squashed product of the following commits: * docs: adds `README.md` header image * docs: updates `README.md` with new information, deduplicates content * revise: add @jdidion's suggestions * revise: one sentence per line Co-authored-by: John Didion --- .github/assets/readme-header.png | Bin 0 -> 44763 bytes README.md | 171 +++++++++---------------------- 2 files changed, 47 insertions(+), 124 deletions(-) create mode 100644 .github/assets/readme-header.png diff --git a/.github/assets/readme-header.png b/.github/assets/readme-header.png new file mode 100644 index 0000000000000000000000000000000000000000..e4b8f6d2a94eb91bcbf3aca368d7b710f5f572bc 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z8^Q-$J$;|eyj2Tl20>3nax{@kVk(^`$nOGnf|81uvNWAtat37mdZ?_$;i)di9c%%( zAz)61YZ8P{{44{^c#dmg1rv9P2)$)bK>5wIra=0ZpE-cf8GCY1gG{auzxwWA3B}H$ zJ72+)K3ct)1|hk*$=ez1y51dgm}ETJ*}3vy;sVK8zXz$TYa@r8hHM|VIcFm0UL9x3 z`Gr2{iQ8Q<4nMwAUKCE4g;!BAq3G{3vCtwy5n&fwXoK+5$wWiX8%Ko?MRYALyp=OW zH|BAVk3+u;9ThS%otp-8g)eDZQiE@ein;9G5~qri(o%AL{*T_pz~PuC9V40J|2g%H zh012R>MKyAV_`5B<(0m_Q@sW}-MNv93N@>fBSU3#)!x6Dra6YcqGD)^T07%?IF7CY zTn`nGC@C4&>2x~cZiSh6J2_JE3FWWdN}RIZLF5j|U{O6Wai+C!@Xiyg;!8N@d50t_ zZIxK*ZHoT-v-*4(d4)>%qf*)QY{%M-GNP_B{|M4CixVQ_?7Cn34%kYN#xAsJb8|g= z+6qRc{OVlp|8do4jhGnL+|)Evnqw8<=jfLf_B(eeMn^{@29CjhgF36rm-Opie?-hasH1<;i&4|--E$miE0W~7>f;%p)JB^;+>MMMK2N(3r!lwL^!(TXc}e9YNFEdia?| z?I53ubkl{&@WG*!XD1kkpJ|R6yZ5wypHa9Q<_A}IH^bb>M`n?fW9o*eq_J?`jFtCp UCU~hlL*DV1ff + + -The **Workflow Description Language (WDL)** is an open standard for describing data processing workflows with a human-readable and writeable syntax. -WDL makes it straightforward to define analysis tasks, connect them together in workflows, and parallelize their execution. -The language strives to be accessible and understandable to all manner of users, including programmers, analysts, and operators of a production system. -The language enables common patterns, such as scatter-gather and conditional execution, to be expressed simply. -WDL is designed for portability, and there are several [implementations](#execution-engines-and-platforms) to choose from that run in a variety of environments, including HPC systems and cloud platforms. +
-## Versioning +The **Workflow Description Language (WDL)** (pronounced as _/hwɪdl/_ or "whittle" with a 'd') is an open standard for describing data processing workflows using a human-readable/writeable syntax. +It introduces a domain-specific language that aims to provide simple but powerful facilities for (a) defining atomic units of computation (a `task`), (b) for connecting those atomic units together into a larger computation graph (a `workflow`), and (c) for effortlessly scaling the execution of these graphs in multiple environments. -WDL versioning follows [semantic versioning](https://semver.org) conventions. +Most fundamentally, WDL differentiates itself from other workflow languages by focusing on ease of implementation and accessibility to a wide range of users, including software engineers, domain experts (e.g., biologists), and operators of production computational systems. +Furthermore, idiomatic workflow execution patterns, such as conditional execution, dynamic resource allocation, and scatter-gather operations, are simply expressed. +Last, the language is driven and developed by a community of distributed volunteers as an open standard; +there is no single execution engine, and anyone can build tooling to contribute to the ecosystem. +Today, [several engines and platforms](#execution-engines-and-platforms) exist and cover most execution environments (all major HPCs, all major clouds, local execution). -The WDL *language* has a two-number version (e.g., `1.2`). -An increase in the minor (second) version number (e.g., `1.1` to `1.2`) indicates the addition of, or non-breaking changes to, the language or standard library functions. -An increase in the major (first) version number (e.g., `1.0` to `2.0`) indicates that breaking changes have been made. +## Getting Started -The WDL *specification* has a three-number version (e.g., `1.2.0`). -The specification version tracks the language version, but there may also be patch releases (indicated by a change to the patch, or third, version number) that include fixes for typos, additional examples, or non-breaking clarifications of ambiguous language. +If you're new to WDL, welcome 👋. We _highly_ recommend that you read the [getting started documentation][wdl-docs] to learn how to write tasks and workflows. -## Language Specifications - -The WDL specification contains all relevant information for users and developers, including those wanting to implement an execution engine. -This GitHub project uses the branch for the current version of the specification as its primary branch, so you will always see the current version of the specification so long as you visit this project's [root URL](https://github.com/openwdl/wdl). -Users are strongly encouraged to use the current version of the specification unless absolutely necessary. - -This branch is for version **1.2** of the [WDL language specification](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md). -All development of new *non-breaking* features should be done against this branch. - -Previous versions of the spec can be found here: - -- [1.1](https://github.com/openwdl/wdl/blob/wdl-1.1/SPEC.md) -- [1.0](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md) - -There are a number of draft versions that correspond to initial efforts at creating WDL. -While these are functional specifications, they should not be considered feature complete, and they contain many bugs and irregularities. - -- [draft-3](https://github.com/openwdl/wdl/blob/main/versions/draft-3/SPEC.md) -- [draft-2](https://github.com/openwdl/wdl/blob/main/versions/draft-2/SPEC.md) -- [draft-1](https://github.com/openwdl/wdl/blob/main/versions/draft-1/SPEC.md) - -The next *major* version of the specification is [2.0](https://github.com/openwdl/wdl/blob/wdl-2.0/SPEC.md). -All development of new *breaking* features should be done against that branch. - -## Community and Support +### Join the community The WDL community depends on your involvement to thrive. You are encouraged to ask questions, help other users, and make contributions where you can. -Interactions occur primarily on [GitHub](https://github.com/openwdl/wdl) and [Slack](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw). -The WDL community also has an official [blog](https://dev.to/openwdl) where announcements are made. - -### Asking a Question - -- Search in the [discussions](https://github.com/openwdl/wdl/discussions) to see if the question has been asked already; if not, start a new discussion. -- Join our [Slack](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw) and ask in the `#support` channel. -- Search the [Bioinformatics Stack Exchange](https://bioinformatics.stackexchange.com/search?q=wdl) for previously answered questions, or ask a new question. -- Search the [Google Group](https://groups.google.com/a/openwdl.org/forum/#!forum/community) for previously answered questions. This group is largely inactive, so you're encoraged to ask new questions in one of the above places instead. - -### Bugs and New Features - -- Search for an existing [issue](https://github.com/openwdl/wdl/issues). If your issue has not already been reported, create a new one. -- For feature reqeusts, you are encoraged to first start a discussion at one of the places listed above to get feedback from the community. -- If you'd like to provide a fix/implementation for an issue, please read about [contributing](#contributing) before submitting a [pull request](https://github.com/openwdl/wdl/pulls). - -### Documentation +Interactions occur primarily on [GitHub][github-main] and [Slack][join-slack]. +The WDL community also has an official [website](https://openwdl.org/) and [blog](https://openwdl.org/blog/) that you can follow to stay up to date. -- [wdl-docs](https://docs.openwdl.org/en/stable/) -- [learn-wdl](https://github.com/openwdl/learn-wdl) -- [WDL Resources](https://support.terra.bio/hc/en-us/sections/360007274612-WDL-Resources) provided by Terra (a product of the Broad Institute) +* **If you have questions about using WDL,** search in the [discussions](https://github.com/openwdl/wdl/discussions) to see if the question has been asked already; if not, feel free to start a new discussion. You can also join the `#support` channel on [Slack][join-slack] to ask more transient questions. +* **If you are a user of an execution engine and encounter a bug or want to request a feature,** you are encouraged to file an issue on the relevant execution engine's repository. Please do not file these types of questions/requests on this repository. +* **If you are an implementor and need clarification on the specification or want to request a feature to be added to the WDL language,** please file an issue on the WDL specification's [GitHub issues][github-issues] page. +- **If you'd like to contribute to the WDL specification,** please read the [contributing](#contributing) section before submitting a pull request. -## Published Workflows +## Specification -The following are collections of open-source WDL workflows. -The WDL task or workflow you need may already be available in one of these repositories, or you may find a similar workflow and customize it to your needs. - -- [Dockstore](https://dockstore.org/search?entryType=workflows&descriptorType=WDL&searchMode=files) -- [BioWDL](https://github.com/biowdl) -- [Broad Institute WARP](https://broadinstitute.github.io/warp/docs/get-started/) -- [GATK Workflows](https://github.com/gatk-workflows/) -- [ENCODE](https://www.encodeproject.org/pipelines/) -- [Terra](https://app.terra.bio) (requires registration) - -## Software and Tools - -### Execution Engines and Platforms - -WDL does not have an official implementation. -Third parties are relied upon to provide installable software or hosted platforms that interpret and execute WDL workflows and tasks. -Although WDL does not yet have an official compliance program or certification process, implementers are expected to design their tools according to the specification so as to maximize the portability of workflows across implementations. -Nonetheless, implementers may provide additional optional features specific. -Please see the documentation associated with each tool/platform for information on available execution options and support. - -| Implementation | Requires Installation | Local Execution | HPC | Cloud | -| ------------------------------------------------------------------------------ | --------------------- | --------------- | ----- | --------------------- | -| [AWS HealthOmics](https://docs.aws.amazon.com/omics/latest/dev/workflows.html) | No | No | No | AWS | -| [Cromwell](https://github.com/broadinstitute/cromwell) * | Yes | Yes | Many | AWS Batch, Azure, GCP | -| [dxCompiler](https://github.com/dnanexus/dxCompiler) | Yes | No | No | DNAnexus | -| [MiniWDL](https://github.com/chanzuckerberg/miniwdl) | Yes | Yes | SLURM | AWS Batch | -| [Terra](https://terra.bio/) | No | No | No | Azure, GCP | - -\* Also see [WDL Runner](https://github.com/broadinstitute/wdl-runner), a script for launch WDL workflows on GCP using Cromwell - -### Grammars, Parsers, and Language Support - -- The WDL [parsers repository](https://github.com/openwdl/wdl-parsers/) provides grammar definitions in various formats and generated parsers for various languages. -- [MiniWDL](https://github.com/chanzuckerberg/miniwdl) provides python bindings for WDL as well as commandline tools for validation, linting, and generating workflow input templates. -- [WOMTool](https://cromwell.readthedocs.io/en/stable/WOMtool/) is a standalone Java tool for WDL parsing, validating, linting, and diagramming. -- [wdlTools](https://github.com/dnanexus/wdlTools) - provides 1) a parser Java/Scala library, based on the [ANTLR4 grammars](https://github.com/openwdl/wdl-parsers) grammars, for WDL draft-2, 1.0, 1.1, and 2.0; and 2) command-line tools for sytanx checking, type-checking, linting, code formatting (including upgrading from older to newer WDL versions), generating documentation, and executing WDL tasks locally. -- [sprocket](https://github.com/stjude-rust-labs/sprocket) a package manager and linter for WDL files. - -### IDE Support - -| IDE | Tool | -| ------------------ | ------------------------------------------------------------------------------------------------ | -| Emacs | [poly-wdl](https://github.com/jmonlong/poly-wdl) | -| Emacs | [wdl-mode](https://github.com/zhanxw/wdl-mode) | -| JetBrains | [Winstanly](https://plugins.jetbrains.com/plugin/8154-winstanley-wdl) | -| Sublime | [WDL Syntax Highlighter](https://github.com/broadinstitute/wdl-sublime-syntax-highlighter) | -| Vim | [vim-wdl](https://github.com/broadinstitute/vim-wdl) | -| Visual Studio Code | [WDL Syntax Highlighter](https://marketplace.visualstudio.com/items?itemName=broadinstitute.wdl) | +The WDL specification contains all relevant information for users and developers, including those wanting to implement an execution engine. +This GitHub project uses the branch for the current version of the specification as its primary branch, so you will always see the current version of the specification so long as you visit this project's [root URL][github-main]. +Users are strongly encouraged to use the current version of the specification unless absolutely necessary. -### Documentation +* This branch is for version `1.2` of the specification ([link](https://github.com/openwdl/wdl/blob/wdl-1.2/SPEC.md)). All development of new *non-breaking* features should be done against this branch. +* The next major version of the specification is version `2.0` ([link](https://github.com/openwdl/wdl/blob/wdl-2.0/SPEC.md)). All development of new *breaking* features should be done against that branch. -- [wdl-aid](https://github.com/biowdl/wdl-aid) generates documentation for the inputs of WDL workflows, based on the parameter_meta information defined in the WDL file. -- [wdldoc](https://github.com/stjudecloud/wdldoc) +If desired, previous versions of the spec can be found on the [GitHub branches page][github-branches]. -### Testing +### Versioning -- [wdl-tests](https://github.com/openwdl/wdl-tests) is a collection of test cases for WDL implementations. A specification is provided for writing new tests that are compatible with automated testing frameworks. -- [Pytest-workflow](https://github.com/LUMC/pytest-workflow) is a implementation-agnostic workflow tester. It can be used with both Cromwell and MiniWDL. Uses pytest as the underlying test framework. Tests can be specified in either YAML format or python code. -- [Pytest-wdl](https://github.com/EliLillyCo/pytest-wdl) is a plugin for the pytest unit testing framework that enables testing of WDL tasks and workflows. Tests can be specified in either YAML format or python code. +All products of the WDL project, including the specification, follow [semantic versioning](https://semver.org). +That being said, the version of the WDL _language_ and the version of the WDL _specification_ are distinct: -### Packaging +* The WDL _language_ has a two-number version (e.g., `1.2`). An increase in the minor (second) version number (e.g., `1.1` to `1.2`) indicates the addition of, or non-breaking changes to, the language or standard library functions. An increase in the major (first) version number (e.g., `1.0` to `2.0`) indicates that breaking changes have been made. -- [miniwdl zip](https://miniwdl.readthedocs.io/en/latest/zip.html) generates a ZIP file including a given WDL source code file and any other WDL files it imports. The ZIP file can be supplied directly to miniwdl run, which can extract it automatically. -- [wdl-packager](https://github.com/biowdl/wdl-packager) packages a workflow and all of its imports into a zip file. The zip can be used as an imports zip package for cromwell. The utility can add non-WDL files (such as the license) to the zip package and provides options to package the zip in a binary reproducible way. +* The WDL _specification_ has a three-number version (e.g., `1.2.0`). The specification version tracks the language version, but there may also be patch releases (indicated by a change to the patch, or third, version number) that include fixes for typos, additional examples, or non-breaking clarifications of ambiguous language. -## Contributing +### Contributing WDL only advances through community contributions. While participating in discussions and submitting issues are great ways to be involved, help is also needed to implement changes to the specification. For more information on how you can contribute, please read the [Contributing](CONTRIBUTING.md) guide. -### RFC Process +### Governance + +The WDL specification is entirely community driven; +however, it is overseen by a [Governance committee](GOVERNANCE.md). +If you are interested in being involved in WDL governance, please join the [Slack][join-slack] and post a message in the `#general` channel. + +### License -Submitted [pull requests](https://github.com/openwdl/wdl/pulls) are subject to the [RFC Process](RFC.md). -Please review and familiarize yourself with the process if you would like to see changes submitted to the specification. +The WDL specification is made available to you under the permissive [BSD 3-Clause License](./LICENSE). -## Governance +© 2024 The OpenWDL Developers -The WDL specification is entirely community driven; however, it is overseen by a [Governance committee](GOVERNANCE.md). -If you are interested in being involved in WDL governance, please join the [Slack](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw) and post a message in the `#general` channel. +[github-main]: https://github.com/openwdl/wdl +[github-branches]: https://github.com/openwdl/wdl/branches +[github-issues]: https://github.com/openwdl/wdl/issues +[join-slack]: https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw +[wdl-docs]: https://docs.openwdl.org/en/stable From ea49e2ed5de9e63c2d4d5b7031396c4b724c4ff0 Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Wed, 22 Jan 2025 23:50:36 -0600 Subject: [PATCH 06/28] chore: adds new pull request template --- .github/PULL_REQUEST_TEMPLATE.md | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9ba92c3e..cbe68768 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,4 +1,16 @@ +_Describe the change you implemented and link to any relevant issues._ -### Checklist -- [ ] Pull request details were added to CHANGELOG.md -- [ ] Valid examples WDL's were added or updated to the SPEC.md (see the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) on writing markdown tests) +Before submitting this PR, please make sure: + +- [ ] You have added a few sentences describing the PR here. +- [ ] You have added yourself or the appropriate individual as the assignee. +- [ ] You have updated the `README.md` or other documentation to account for these + changes (when appropriate). +- [ ] You have updated the `CHANGELOG.md` describing the change and linking back to your + pull request. +- [ ] You have read and agree to the + [`CONTRIBUTING.md`](https://github.com/openwdl/wdl/blob/wdl-1.2/CONTRIBUTING.md) + document. +- [ ] You have added or updated relevant example WDL tests to the specification. + - See the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) + for more details. From bcd123c12cefd71af51bf5d74ef8a8de44d0d3aa Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Sun, 26 Jan 2025 08:52:18 -0600 Subject: [PATCH 07/28] chore: further tweak the pull request template --- .github/PULL_REQUEST_TEMPLATE.md | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index cbe68768..bddc20ac 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -6,11 +6,7 @@ Before submitting this PR, please make sure: - [ ] You have added yourself or the appropriate individual as the assignee. - [ ] You have updated the `README.md` or other documentation to account for these changes (when appropriate). -- [ ] You have updated the `CHANGELOG.md` describing the change and linking back to your - pull request. -- [ ] You have read and agree to the - [`CONTRIBUTING.md`](https://github.com/openwdl/wdl/blob/wdl-1.2/CONTRIBUTING.md) - document. +- [ ] You have updated the `CHANGELOG.md` describing the change and linking back to your pull request. +- [ ] You have read and agree to the [`CONTRIBUTING.md`](https://github.com/openwdl/wdl/blob/wdl-1.2/CONTRIBUTING.md) document. - [ ] You have added or updated relevant example WDL tests to the specification. - - See the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) - for more details. + - See the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) for more details. From dc848bd283a526efb241256c777344fa530bcc53 Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Mon, 27 Jan 2025 20:16:16 -0600 Subject: [PATCH 08/28] chore: moves governance information to `openwdl/governance` --- CONTRIBUTING.md | 30 ------------------------------ GOVERNANCE.md | 38 -------------------------------------- README.md | 28 ++++++++++++++-------------- RFC.md | 16 ---------------- 4 files changed, 14 insertions(+), 98 deletions(-) delete mode 100644 CONTRIBUTING.md delete mode 100644 GOVERNANCE.md delete mode 100644 RFC.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md deleted file mode 100644 index c98cf977..00000000 --- a/CONTRIBUTING.md +++ /dev/null @@ -1,30 +0,0 @@ -# Contributing to WDL - -WDL strives to be community driven and thus relies on suggestions and assistance from people such as yourself. We welcome any contribution that you are willing to provide whether it be in the form of syntax suggestions, feature requests, documentation help, or simply pointing out our ~~tyops~~ typos. All that we ask is that you agree to the following [contributor agreement](#contributor-agreement) and follow a [few guidelines](#how-to-contribute). - -# Contributor agreement - -I understand that WDL is a community-driven standard. Any ideas or suggestions I provide may be used by the community and may become part of the official WDL specification under the [BSD 3-clause license](https://github.com/broadinstitute/wdl/blob/develop/LICENSE). I attest that all contributions are my own and not copyrighted by another party. - -# How to contribute -## Contributions to WDL discussions - -WDL is the bioinformatics workflow language meant to be written and read by humans. In order to achieve this goal we rely on actual humans to help keep us on the right course. Fellow WDL enthusiasts debate the finer points of syntax in the [WDL Slack](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw) and everyone is invited to participate (registration required). - -## Contributions to the WDL ecosystem - -As WDL increases in popularity, a number of people are [building tools](README.md#software-and-tools) to make it easier to interact with WDL or platforms that support it. If you've created something which you think would be useful we'd love to hear about it! We can help you help us help everyone. - -## Contributions to the documentation, code, etc - -We welcome any contribution to the WDL [Github repository](https://github.com/broadinstitute/wdl), whether it be to the [specification](https://github.com/broadinstitute/wdl/blob/develop/SPEC.md), [example scripts](https://github.com/broadinstitute/wdl/tree/develop/scripts), [syntax highlighters](https://github.com/broadinstitute/wdl/tree/develop/highlighters), or anything we haven't yet thought of. To do this, first fork then clone the repo: - - git clone git@github.com:your-username/wdl.git - -Make your change and then push your changes to the fork and [submit a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) - -## RFC Process - -Any changes submitted to the WDL Specification are subject to the [RFC Process](RFC.md). Please review and familiarize yourself with the process if you would like to see changes submitted to the specification. - - \ No newline at end of file diff --git a/GOVERNANCE.md b/GOVERNANCE.md deleted file mode 100644 index b2a638d8..00000000 --- a/GOVERNANCE.md +++ /dev/null @@ -1,38 +0,0 @@ -OpenWDL Governance and Process -============================== - - -WDL has a community-driven development process where most decisions are made through consensus, under the stewardship of a 'core team'. The core team is responsible for steering the design and development process, overseeing the introduction of new features, setting priorities and release schedule, and ultimately making decisions for the rare instances where there is no community consensus. - -Current core team members are: - -| Name | Organization | github | -| :-------------------- | :------------------------------------ | :-------------------------------------------------- | -| John Didion | Fulcrum Genomics | [jdidion](https://github.com/jdidion) | -| Taylor Firman | Fred Hutch | [tefirman](https://github.com/tefirman) | -| Michael Franklin | Centre for Population Genomics | [illusional](https://github.com/illusional) | -| Jeff Gentry | Fulcrum Genomics | [geoffjentry](https://github.com/geoffjentry) | -| Peter Huene | St. Jude Children's Research Hospital | [peterhuene](https://github.com/peterhuene) | -| Mike Lin | Chan Zuckerberg Initiative | [mlin](https://github.com/mlin) | -| Christopher Llanwarne | Broad Institute | [cjllanwarne](https://github.com/cjllanwarne) | -| Patrick Magee | DNAstack | [patmagee](https://github.com/patmagee) | -| Venkat Malladi | Microsoft | [vsmalladi](https://github.com/vsmalladi) | -| Clay McLeod | St. Jude Children's Research Hospital | [claymcleod](https://github.com/claymcleod) | -| Brian O'Connor | University of California, Santa Cruz | [briandoconnor](https://github.com/briandoconnor) | -| Lee Pang | Amazon | [wleepang](https://github.com/wleepang) | -| Mark Schreiber | Amazon | [markjschreiber](https://github.com/markjschreiber) | -| Ruben Vorderman | Leiden University Medical Center | [rhpvorderman](https://github.com/rhpvorderman) | - -At the core group's discretion a new member may be added by a majority vote. This addition will be done to recognize **significant** contributions to the community. *Contributions* include such things as: - - - Active participation in discussions, mailing list, forums - - Community building efforts - - Helping with documentation, standards documents, etc - - Building supporting software and tooling - -Generally members are only removed at their own request are due to very long term inactivity. In extreme circumstances the core group can vote to remove a member. - - -# RFC Process - -Any changes submitted to the WDL Specification are subject to the [RFC Process](RFC.md). Please review and familiarize yourself with the process if you would like to see changes submitted to the specification. diff --git a/README.md b/README.md index c4008815..01d5fd1e 100644 --- a/README.md +++ b/README.md @@ -7,28 +7,22 @@ The **Workflow Description Language (WDL)** (pronounced as _/hwɪdl/_ or "whittle" with a 'd') is an open standard for describing data processing workflows using a human-readable/writeable syntax. It introduces a domain-specific language that aims to provide simple but powerful facilities for (a) defining atomic units of computation (a `task`), (b) for connecting those atomic units together into a larger computation graph (a `workflow`), and (c) for effortlessly scaling the execution of these graphs in multiple environments. + Most fundamentally, WDL differentiates itself from other workflow languages by focusing on ease of implementation and accessibility to a wide range of users, including software engineers, domain experts (e.g., biologists), and operators of production computational systems. Furthermore, idiomatic workflow execution patterns, such as conditional execution, dynamic resource allocation, and scatter-gather operations, are simply expressed. Last, the language is driven and developed by a community of distributed volunteers as an open standard; there is no single execution engine, and anyone can build tooling to contribute to the ecosystem. -Today, [several engines and platforms](#execution-engines-and-platforms) exist and cover most execution environments (all major HPCs, all major clouds, local execution). - -## Getting Started +Today, [several engines and platforms] exist and cover most execution environments (all major HPCs, all major clouds, local execution). -If you're new to WDL, welcome 👋. We _highly_ recommend that you read the [getting started documentation][wdl-docs] to learn how to write tasks and workflows. +## Join the community -### Join the community +If you're new to WDL, welcome 👋. We _highly_ recommend that you read the [getting started documentation] to learn how to write tasks and workflows. The WDL community depends on your involvement to thrive. -You are encouraged to ask questions, help other users, and make contributions where you can. +You are encouraged to [ask questions], help other users, and make contributions where you can. Interactions occur primarily on [GitHub][github-main] and [Slack][join-slack]. The WDL community also has an official [website](https://openwdl.org/) and [blog](https://openwdl.org/blog/) that you can follow to stay up to date. -* **If you have questions about using WDL,** search in the [discussions](https://github.com/openwdl/wdl/discussions) to see if the question has been asked already; if not, feel free to start a new discussion. You can also join the `#support` channel on [Slack][join-slack] to ask more transient questions. -* **If you are a user of an execution engine and encounter a bug or want to request a feature,** you are encouraged to file an issue on the relevant execution engine's repository. Please do not file these types of questions/requests on this repository. -* **If you are an implementor and need clarification on the specification or want to request a feature to be added to the WDL language,** please file an issue on the WDL specification's [GitHub issues][github-issues] page. -- **If you'd like to contribute to the WDL specification,** please read the [contributing](#contributing) section before submitting a pull request. - ## Specification The WDL specification contains all relevant information for users and developers, including those wanting to implement an execution engine. @@ -53,22 +47,28 @@ That being said, the version of the WDL _language_ and the version of the WDL _s WDL only advances through community contributions. While participating in discussions and submitting issues are great ways to be involved, help is also needed to implement changes to the specification. -For more information on how you can contribute, please read the [Contributing](CONTRIBUTING.md) guide. +For more information on how you can contribute, please read the [Contributing] guide. ### Governance The WDL specification is entirely community driven; -however, it is overseen by a [Governance committee](GOVERNANCE.md). +however, it is overseen by a [governance committee and process]. If you are interested in being involved in WDL governance, please join the [Slack][join-slack] and post a message in the `#general` channel. ### License The WDL specification is made available to you under the permissive [BSD 3-Clause License](./LICENSE). -© 2024 The OpenWDL Developers +© 2024-Present The OpenWDL Developers [github-main]: https://github.com/openwdl/wdl [github-branches]: https://github.com/openwdl/wdl/branches [github-issues]: https://github.com/openwdl/wdl/issues [join-slack]: https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw [wdl-docs]: https://docs.openwdl.org/en/stable +[Contributing]: https://github.com/openwdl/governance/blob/main/CONTRIBUTING.md +[several engines and platforms]: https://docs.openwdl.org/getting-started/ecosystem.html +[getting started documentation]: https://docs.openwdl.org/getting-started/quickstart.html +[contributing]: https://github.com/openwdl/governance/blob/main/CONTRIBUTING.md +[governance committee and process]: https://github.com/openwdl/governance/blob/main/README.md +[ask questions]: https://docs.openwdl.org/getting-started/getting-help.html diff --git a/RFC.md b/RFC.md deleted file mode 100644 index 26fb6147..00000000 --- a/RFC.md +++ /dev/null @@ -1,16 +0,0 @@ -RFC Process ------------ - -Most technical decisions are decided through the "RFC" ([Request for Comments](https://en.wikipedia.org/wiki/Request_for_Comments)) process. Small changes, such as minor grammatical edits to the specification, do not need to need to follow the RFC process. However, if one intends to make a substantive change to the WDL specification , the following process should be adhered to: - -1. Ideally have an informal discussion of the topic on [Slack](https://join.slack.com/t/openwdl/shared_invite/zt-ctmj4mhf-cFBNxIiZYs6SY9HgM9UAVw) and/or [GitHub discussions](https://github.com/openwdl/wdl/discussions) in order to gauge basic viability. As a rule of thumb, receiving encouraging feedback from long-standing community members is a good indication that the RFC is worth pursuing. -2. Write up a formal proposal, including requested changes to the current specification, as a pull request on GitHub -3. A core team member will be assigned as the *shepherd* of this RFC. The shepherd shall be responsible for keeping the discussion moving and ensuring all concerns are responded to. -4. Work to build broad support from the community. Encouraging people to comment, show support, show dissent, etc. Ultimately the level of community support for a change will decide its fate. -5. RFCs rarely go through this process unchanged, especially as alternatives and drawbacks are discovered. You can make edits to the RFC to clarify or change the design, but make changes as new commits to the pull request, and leave a comment on the pull request explaining your changes. Specifically, do not squash or rebase commits after they are visible on the pull request. -6. Every significant addition or change to the spec will require a test case to be accepted. See the [testing README](tests/README.md) for details on how to write tests. -7. When it appears that a discussion is no longer progressing in a constructive way, or a general consensus has been reached, the shepherd will make an official summary on where the consensus has wound up. -8. The shepherd will put out an official call for votes. This call shall be advertised broadly and will last ten calendar days. Any interested member may vote via +1/-1. -9. After the voting process is complete the core group shall decide to officially approve this RFC. It is expected that barring extreme circumstances this is a rubber stamp of the voting process. An example of an exceptional case would be if representatives for every WDL implementation vote against the feature for feasibility reasons. - -When an RFC is approved it will become part of the current draft version of the specification. This will allow time for implementers to verify feasibility and cutting edge users to get used to the new syntax. In order to prevent untested features from entering into an official specification version at least one WDL implementation must support a feature before it’s allowed to be merged into the current draft version. 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-1,5 +1,5 @@
- +

From 7e9ebb4c8d33796efb11c193eadcc67a98c9dfdc Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 12 Feb 2025 16:01:24 -0600 Subject: [PATCH 10/28] Fix examples and tests for wdl 1.2. --- SPEC.md | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/SPEC.md b/SPEC.md index dfc4c5a4..be41f0d5 100644 --- a/SPEC.md +++ b/SPEC.md @@ -730,13 +730,13 @@ In multi-line strings, leading *whitespace* is removed according to the followin ```json { - "multiline_strings2.hw0": "hello world" - "multiline_strings2.hw1": "hello world" - "multiline_strings2.hw2": "hello world" - "multiline_strings2.hw3": "hello world" - "multiline_strings2.hw4": "hello world" - "multiline_strings2.hw5": "hello world" - "multiline_strings2.hw6": "hello world" + "multiline_strings2.hw0": "hello world", + "multiline_strings2.hw1": "hello world", + "multiline_strings2.hw2": "hello world", + "multiline_strings2.hw3": "hello world", + "multiline_strings2.hw4": "hello world", + "multiline_strings2.hw5": "hello world", + "multiline_strings2.hw6": "hello world", "multiline_strings2.not_equivalent": "hello \\\n world" } ``` @@ -799,9 +799,9 @@ Common leading whitespace is also removed from blank lines that contain whitespa ```json { - "multiline_strings3.multi_line_A": "\nthis is a\n\n multi-line string\n" - "multiline_strings3.multi_line_B": "\nthis is a\n\n multi-line string\n" - "multiline_strings3.multi_line_C": "\nthis is a\n\n multi-line string\n" + "multiline_strings3.multi_line_A": "\nthis is a\n\n multi-line string\n", + "multiline_strings3.multi_line_B": "\nthis is a\n\n multi-line string\n", + "multiline_strings3.multi_line_C": "\nthis is a\n\n multi-line string\n", "multiline_strings3.multi_line_D": "\nthis is a\n\n multi-line string\n" } ``` @@ -4017,6 +4017,7 @@ The environment variable should be evaluated by the engine prior to injecting it
+Example: environment_variable_should_echo.wdl ```wdl version 1.2 @@ -4045,6 +4046,7 @@ workflow environment_variable_should_echo { output { String out = test.out } +} ```

@@ -8855,7 +8857,7 @@ Example output: "write_tsv.structs_default": ["first", "one", "un"], "write_tsv.structs_no_header": ["two", "deux"], "write_tsv.structs_header": ["second", "two", "deux"], - "write_tsv.structs_user_header": ["no3", "three", "trois"], + "write_tsv.structs_user_header": ["no3", "three", "trois"] } ``` @@ -10949,7 +10951,7 @@ For example, if the first argument is a `Map[String, Map[String, Int]]` and the "test_contains_key.i1": 1, "test_contains_key.i2": null, "test_contains_key.phone1": "123-456-7890", - "test_contains_key.phone2": null, + "test_contains_key.phone2": null } ```

@@ -11220,7 +11222,7 @@ Example output: "test_length.ylen": 3, "test_length.zlen": 0, "test_length.mlen": 2, - "test_length.slen": 5, + "test_length.slen": 5 } ```

From 3f20ccae1cb391549ba4a37f288b615279e8525b Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Thu, 13 Feb 2025 12:50:16 -0600 Subject: [PATCH 11/28] Add in chagnelon about changes. --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a68714c6..61fb2946 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,11 @@ Keep the changelog pleasant to read in the text editor: + Properly indent blocks. --> +version 1.2.1 +--------------------------- + +* Include fixes to examples that don't comile in `wdl-tests` + version 1.2.0 --------------------------- From 91b60171b1ad8cf2b2abd2edd2797b9f6f56572a Mon Sep 17 00:00:00 2001 From: Clay McLeod Date: Sat, 15 Feb 2025 21:46:23 -0600 Subject: [PATCH 12/28] ci: adds issue triaging ci workflow --- .github/workflows/triage.yml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .github/workflows/triage.yml diff --git a/.github/workflows/triage.yml b/.github/workflows/triage.yml new file mode 100644 index 00000000..991a79a1 --- /dev/null +++ b/.github/workflows/triage.yml @@ -0,0 +1,20 @@ +name: Triage issues + +on: + issues: + types: + - reopened + - opened + +jobs: + label_issues: + runs-on: ubuntu-latest + permissions: + issues: write + steps: + - run: gh issue edit "$NUMBER" --add-label "$LABELS" + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_REPO: ${{ github.repository }} + NUMBER: ${{ github.event.issue.number }} + LABELS: S01-needs-triage From 682b67f5bdf452d50355e690a99ffada60ef94be Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 19 Feb 2025 13:14:59 -0600 Subject: [PATCH 13/28] Fix json formating for running tests as valid input. --- SPEC.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SPEC.md b/SPEC.md index 33b53a29..05da81b2 100644 --- a/SPEC.md +++ b/SPEC.md @@ -12312,7 +12312,7 @@ Example input: ```json { - "serde_map_tsv.items": { + "items": { "a": "b", "c": "d", "e": "f" @@ -12403,7 +12403,7 @@ Example input: ```json { - "serde_map_json.read_quality_scores": { + "read_quality_scores": { "read1": 32, "read2": 41, "read3": 55 From cc4e729ada642ffdab000806f31ecdfe667bb476 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 19 Feb 2025 13:44:49 -0600 Subject: [PATCH 14/28] Tail was wrong the tail of cities is Chicago and Piscataway. --- SPEC.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index 05da81b2..c94c202f 100644 --- a/SPEC.md +++ b/SPEC.md @@ -12101,7 +12101,7 @@ Example output: ```json { "serde_pair.tails_of_two": { - "Houston": "Chicago" + "Chicago": "Piscataway" } } ``` From d5e4da3f85fdfc2177651e8ddfb0c3f582cf20e9 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 19 Feb 2025 14:34:32 -0600 Subject: [PATCH 15/28] Fix input examples to match task level inputs. --- SPEC.md | 80 ++++++++++++++++++++++++++++----------------------------- 1 file changed, 40 insertions(+), 40 deletions(-) diff --git a/SPEC.md b/SPEC.md index c94c202f..61de8baf 100644 --- a/SPEC.md +++ b/SPEC.md @@ -1061,7 +1061,7 @@ Example input: ```json { - "sum.ints": ["0", "1", "2"] + "ints": ["0", "1", "2"] } ``` @@ -2112,7 +2112,7 @@ Example input: ```json { - "expressions.x": 5 + "x": 5 } ``` @@ -2980,8 +2980,8 @@ Example input: ```json { - "flags.infile": "greetings.txt", - "flags.pattern": "world" + "infile": "greetings.txt", + "pattern": "world" } ``` @@ -3117,8 +3117,8 @@ Example input: ```json { - "true_false_ternary.message": "hello world", - "true_false_ternary.newline": false + "message": "hello world", + "newline": false } ``` @@ -3665,7 +3665,7 @@ Example input: ```json { - "task_inputs.i": 1 + "i": 1 } ```

@@ -3793,9 +3793,9 @@ Example input: ```json { - "input_type_quantifiers.a": [], - "input_type_quantifiers.b": ["A", "B"], - "input_type_quantifiers.e": ["C"] + "a": [], + "b": ["A", "B"], + "e": ["C"] } ``` @@ -3961,7 +3961,7 @@ Example input: ```json { - "private_declaration.lines": ["A", "B", "C", "D"] + "lines": ["A", "B", "C", "D"] } ``` @@ -4286,7 +4286,7 @@ Example input: ```json { - "test_placeholders.infile": "greetings.txt" + "infile": "greetings.txt" } ``` @@ -4421,7 +4421,7 @@ Example input: ```json { - "python_strip.infile": "comment.txt" + "infile": "comment.txt" } ``` @@ -4482,7 +4482,7 @@ Example input: ```json { - "outputs.t": 5 + "t": 5 } ``` @@ -4546,7 +4546,7 @@ Example input: ```json { - "file_output.prefix": "foo" + "prefix": "foo" } ``` @@ -4594,7 +4594,7 @@ Example input: ```json { - "glob.num_files": 3 + "num_files": 3 } ``` @@ -4702,7 +4702,7 @@ Example input: ```json { - "optional_output.make_example2": false + "make_example2": false } ``` @@ -5441,7 +5441,7 @@ Example input: ```json { - "test_hints.foo": "greetings.txt" + "foo": "greetings.txt" } ``` @@ -5566,7 +5566,7 @@ Example input: ```json { - "input_hint.person": { + "person": { "name": "Joe" } } @@ -5750,8 +5750,8 @@ Example input: ```json { - "ex_paramter_meta.infile": "greetings.txt", - "ex_paramter_meta.lines_only": true + "infile": "greetings.txt", + "lines_only": true } ``` @@ -5917,9 +5917,9 @@ Example input: ```json { - "hisat2.index_tar_gz": "https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz", - "hisat2.sra_acc": "SRR3440404", - "hisat2.max_reads": 10 + "index_tar_gz": "https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz", + "sra_acc": "SRR3440404", + "max_reads": 10 } ``` @@ -6015,14 +6015,14 @@ Example input: ```json { - "gatk_haplotype_caller.bam": "ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam", - "gatk_haplotype_caller.reference": { + "bam": "ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam", + "reference": { "id":"Homo_sapiens_assembly38", "fasta": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta", "index": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai", "dict": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict" }, - "gatk_haplotype_caller.interval": "chr1:1000000-1010000" + "interval": "chr1:1000000-1010000" } ``` @@ -7901,7 +7901,7 @@ Example input: ```json { - "change_extension.prefix": "foo" + "prefix": "foo" } ``` @@ -8130,7 +8130,7 @@ Example input: ```json { - "gen_files.num_files": 2 + "num_files": 2 } ``` @@ -8590,8 +8590,8 @@ Example input: ```json { - "grep.pattern": "world", - "grep.file": "greetings.txt" + "pattern": "world", + "file": "greetings.txt" } ``` @@ -9477,7 +9477,7 @@ Example input: ```json { - "write_object.obj": { + "obj": { "key_1": "value_1", "key_2": "value_2", "key_3": "value_3" @@ -9561,7 +9561,7 @@ Example input: ```json { - "write_objects.obj_array": [ + "obj_array": [ { "key_1": "value_1", "key_2": "value_2", @@ -11792,8 +11792,8 @@ Example input: ```json { - "read_write_primitives.s": "hello", - "read_write_primitives.i": 42 + "s": "hello", + "i": 42 } ``` @@ -11870,8 +11870,8 @@ Example input: ```json { - "serialize_array_delim.infile": "greetings.txt", - "serialize_array_delim.counts": [1, 2] + "infile": "greetings.txt", + "counts": [1, 2] } ``` @@ -11931,8 +11931,8 @@ Example input: ```json { - "serde_array_lines.infile": "greetings.txt", - "serde_array_lines.patterns": ["hello", "world"] + "infile": "greetings.txt", + "patterns": ["hello", "world"] } ``` @@ -12002,7 +12002,7 @@ Example input: ```json { - "serde_array_json.string_to_int": { + "string_to_int": { "a": 1, "b": 2 } From 43ac011e62767d3eb454d831c006e7e7c40e04d8 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 19 Feb 2025 14:48:20 -0600 Subject: [PATCH 16/28] Fix input examples to match task level inputs. --- SPEC.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SPEC.md b/SPEC.md index 61de8baf..3b2eded3 100644 --- a/SPEC.md +++ b/SPEC.md @@ -3337,7 +3337,7 @@ Example input: ```json { - "greet_person.person": { + "person": { "name": { "first": "Richard", "last": "Rich" @@ -4332,7 +4332,7 @@ Example input: ```json { - "bash_variables.str": "hello" + "str": "hello" } ``` From 6c026e286f2be1b5937a044bf4bb5133fa41ebb5 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Thu, 20 Feb 2025 13:28:02 -0600 Subject: [PATCH 17/28] Fix missing output that is missing. --- SPEC.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index 3b2eded3..98387184 100644 --- a/SPEC.md +++ b/SPEC.md @@ -4594,7 +4594,8 @@ Example input: ```json { - "num_files": 3 + "num_files": 3, + "glob.outfiles": ["file_1.txt", "file_2.txt", "file_3.txt"] } ``` From 8b5d118fb054537d6c9e917bdad247a8f062d740 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Thu, 20 Feb 2025 14:33:49 -0600 Subject: [PATCH 18/28] Reverse commit. Should not be an error. --- SPEC.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/SPEC.md b/SPEC.md index 98387184..3b2eded3 100644 --- a/SPEC.md +++ b/SPEC.md @@ -4594,8 +4594,7 @@ Example input: ```json { - "num_files": 3, - "glob.outfiles": ["file_1.txt", "file_2.txt", "file_3.txt"] + "num_files": 3 } ``` From 2d7310bd9a112f5c0fd275dd12c32a64935e7c25 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 25 Feb 2025 23:11:33 -0600 Subject: [PATCH 19/28] Fix examples in spec. --- SPEC.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/SPEC.md b/SPEC.md index 3b2eded3..0bdac1d5 100644 --- a/SPEC.md +++ b/SPEC.md @@ -3803,7 +3803,7 @@ Example output: ```json { - "input_type_quantifiers.lines": ["A", "B", "C"] + "lines": ["A", "B", "C"] } ```

@@ -4499,7 +4499,7 @@ Test config: ```json { - "exclude_output": "csvs" + "exclude_output": "outputs.csvs" } ```

@@ -4610,7 +4610,7 @@ Test config: ```json { - "exclude_output": "outfiles" + "exclude_output": "glob.outfiles" } ```

@@ -4661,7 +4661,7 @@ Test config: ```json { - "exclude_output": "bashrc" + "exclude_output": "relative_and_absolute.bashrc" } ```

@@ -4825,7 +4825,7 @@ Example input: ```json { - "dynamic_container.ubuntu_version": "focal" + "ubuntu_version": "focal" } ``` @@ -5348,7 +5348,7 @@ Example: all_return_codes_task.wdl ```wdl version 1.2 -task multi_return_code { +task all_return_codes_task { command <<< exit 42 >>> @@ -7918,7 +7918,7 @@ Test config: ```json { - "exclude_output": ["data_file"] + "exclude_output": ["change_extension.data_file"] } ```

From 3ea63db5eca57e736da15f2c594cf474e0a16dcd Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 26 Feb 2025 06:34:32 -0600 Subject: [PATCH 20/28] Fix exclusion of output. --- SPEC.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index 0bdac1d5..a3a57475 100644 --- a/SPEC.md +++ b/SPEC.md @@ -4721,7 +4721,7 @@ Test config: ```json { - "exclude_output": ["example1", "file_array"] + "exclude_output": ["optional_output.example1", "optional_output.file_array"] } ```

From ee6f32d5854ab92f7d3da8eccb6c174d5146d264 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Wed, 26 Feb 2025 08:54:56 -0600 Subject: [PATCH 21/28] Fix name of task to test so that it gets parse correctly. --- SPEC.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index a3a57475..21e1f8bb 100644 --- a/SPEC.md +++ b/SPEC.md @@ -6178,7 +6178,7 @@ When a [call statement](#call-statement) needs to refer to a task or workflow in
-Example: call_imported_task.wdl +Example: call_imported.wdl ```wdl version 1.2 From 0688da00b4d7a9ee06e8c88176676c185deb8954 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Fri, 28 Feb 2025 16:20:52 -0600 Subject: [PATCH 22/28] Fix example. --- SPEC.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/SPEC.md b/SPEC.md index 21e1f8bb..eeec3543 100644 --- a/SPEC.md +++ b/SPEC.md @@ -6015,14 +6015,14 @@ Example input: ```json { - "bam": "ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/RMNISTHS_30xdownsample.bam", - "reference": { - "id":"Homo_sapiens_assembly38", - "fasta": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta", - "index": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai", - "dict": "https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict" + "bam": "https://storage.googleapis.com/genomics-public-data/1000-genomes/bam/HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.bam", + "reference": { + "id":"Homo_sapiens_assembly19_1000genomes_decoy", + "fasta": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta", + "index": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai", + "dict": "https://storage.googleapis.com/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict" }, - "interval": "chr1:1000000-1010000" + "interval": "1:12505000-12506000" } ``` @@ -6030,7 +6030,7 @@ Example output: ```json { - "gatk_haplotype_caller.vcf": "HG002.vcf" + "gatk_haplotype_caller.vcf": "HG00107.mapped.ILLUMINA.bwa.GBR.low_coverage.20130415.vcf" } ``` From 997142cb1d314c3a7dc50de29f0213d49ff601d1 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 4 Mar 2025 12:44:30 -0600 Subject: [PATCH 23/28] Fix hisat2 example. Close #707. --- SPEC.md | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/SPEC.md b/SPEC.md index eeec3543..443dcc3c 100644 --- a/SPEC.md +++ b/SPEC.md @@ -5871,7 +5871,9 @@ version 1.2 task hisat2 { input { File index_tar_gz - String sra_acc + File fastq1 + File fastq2 + String sample_name Int? max_reads Int threads = 8 Float memory_gb = 16 @@ -5882,19 +5884,24 @@ task hisat2 { command <<< mkdir "~{index_id}" - tar -C "~{index_id}" --strip-components 2 -xzf "~{index_tar_gz}" + tar -C "~{index_id}" --strip-components 1 -xzf "~{index_tar_gz}" + for i in "${index_id}/genome.*.ht2"; do + num=$(echo $i | sed 's/.*\.\([0-9]\+\)\.ht2/\1/') # Extract the number from the filename + mv "$i" "${index_id}/${index_id}.${num}.ht2" # Rename each file + done hisat2 \ -p ~{threads} \ ~{if defined(max_reads) then "-u ~{select_first([max_reads])}" else ""} \ - -x "~{index_id}" \ - --sra-acc ~{sra_acc} > ~{sra_acc}.sam + -1 ~{fastq1} -2 ~{fastq2} \ + -x "~{index_id}"/"~{index_id}" \ + > ~{sample_name}.sam >>> output { - File sam = "output.sam" + File sam = "~{sample_name}.sam" } - requirements { + runtime { container: "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3" cpu: threads memory: "~{memory_gb} GB" @@ -5907,7 +5914,9 @@ task hisat2 { parameter_meta { index_tar_gz: "Gzipped tar file with HISAT2 index files" - sra_acc: "SRA accession number or reads to align" + fastq1: "The first-end FastQ file." + fastq2: "The second-end FastQ file." + sample_name: "Name of the sample" } } ``` @@ -5918,7 +5927,9 @@ Example input: ```json { "index_tar_gz": "https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz", - "sra_acc": "SRR3440404", + "fastq1": "https://storage.googleapis.com/genomics-public-data/gatk-examples/example1/NA20274/ERR250968_1.filt.fastq.gz", + "fastq2":"https://storage.googleapis.com/genomics-public-data/gatk-examples/example1/NA20274/ERR250968_2.filt.fastq.gz", + "sample_name": "NA20274", "max_reads": 10 } ``` @@ -5927,7 +5938,7 @@ Example output: ```json { - "hisat2.sam": "SRR3440404.sam" + "hisat2.sam": "NA20274.sam" } ``` From e32ba64a598b40d9558edf57397dd65fc754157b Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 4 Mar 2025 13:16:40 -0600 Subject: [PATCH 24/28] Fix some dangling issues. --- SPEC.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/SPEC.md b/SPEC.md index 443dcc3c..5c350c4b 100644 --- a/SPEC.md +++ b/SPEC.md @@ -5885,9 +5885,9 @@ task hisat2 { command <<< mkdir "~{index_id}" tar -C "~{index_id}" --strip-components 1 -xzf "~{index_tar_gz}" - for i in "${index_id}/genome.*.ht2"; do + for i in "~{index_id}/genome.*.ht2"; do num=$(echo $i | sed 's/.*\.\([0-9]\+\)\.ht2/\1/') # Extract the number from the filename - mv "$i" "${index_id}/${index_id}.${num}.ht2" # Rename each file + mv "$i" "~{index_id}/~{index_id}.${num}.ht2" # Rename each file done hisat2 \ -p ~{threads} \ @@ -5989,6 +5989,7 @@ task gatk_haplotype_caller { ln -s ~{reference.fasta} ref/~{reference.id}.fasta ln -s ~{reference.index} ref/~{reference.id}.fasta.fai ln -s ~{reference.dict} ref/~{reference.id}.dict + samtools index ~{bam} gatk --java-options "-Xmx~{memory_gb}g" HaplotypeCaller \ ~{if defined(interval) then "-L ~{select_first([interval])}" else ""} \ -R ref/~{reference.id}.fasta \ From 714a2327d9c3e2d6d8f314c01f49f3a1d40db08f Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 4 Mar 2025 13:36:10 -0600 Subject: [PATCH 25/28] Fix some dangling issues. --- SPEC.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/SPEC.md b/SPEC.md index 5c350c4b..d4cfb1a5 100644 --- a/SPEC.md +++ b/SPEC.md @@ -5885,15 +5885,11 @@ task hisat2 { command <<< mkdir "~{index_id}" tar -C "~{index_id}" --strip-components 1 -xzf "~{index_tar_gz}" - for i in "~{index_id}/genome.*.ht2"; do - num=$(echo $i | sed 's/.*\.\([0-9]\+\)\.ht2/\1/') # Extract the number from the filename - mv "$i" "~{index_id}/~{index_id}.${num}.ht2" # Rename each file - done hisat2 \ -p ~{threads} \ ~{if defined(max_reads) then "-u ~{select_first([max_reads])}" else ""} \ -1 ~{fastq1} -2 ~{fastq2} \ - -x "~{index_id}"/"~{index_id}" \ + -x "~{index_id}"/genome \ > ~{sample_name}.sam >>> From 944ce1b074e0a4099645a2240a394f9e19b7f980 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 8 Apr 2025 09:11:41 -0500 Subject: [PATCH 26/28] Add in null optional type. Will not fail if not present. Closes issue in miniwdl. --- SPEC.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index d4cfb1a5..3e4e6dbe 100644 --- a/SPEC.md +++ b/SPEC.md @@ -1433,12 +1433,22 @@ Example output: "account_number": "123456", "routing_number": 300211325, "balance": 3.5, - "pin_digits": [1, 2, 3, 4] + "pin_digits": [1, 2, 3, 4], + "username": null } }, "test_struct.has_account": true } ``` + +Test config: + +```json +{ + "optional_output": "username" +} +``` +

From 3aea0dca9d0eb7cfcaa5a00b404e38181da8203d Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 8 Apr 2025 09:49:43 -0500 Subject: [PATCH 27/28] Fix spec example. --- SPEC.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SPEC.md b/SPEC.md index 3e4e6dbe..211955f1 100644 --- a/SPEC.md +++ b/SPEC.md @@ -7855,7 +7855,7 @@ workflow test_sub { String chocoearly = sub(chocolike, "late", "early") # I like chocoearly when\nit's early String chocolate = sub(chocolike, "late$", "early") # I like chocolate when\nit's early String chocoearlylate = sub(chocolike, "[^ ]late", "early") # I like chocearly when\nit's late - String choco4 = sub(chocolike, " [:alpha:]{4} ", " 4444 ") # I 4444 chocolate when\nit's late + String choco4 = sub(chocolike, " [[:alpha:]]{4} ", " 4444 ") # I 4444 chocolate when\nit's late String no_newline = sub(chocolike, "\\n", " ") # "I like chocolate when it's late" } } From f9170c5ec211d4d1fec88d75746d9815b26ecb7b Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 8 Apr 2025 10:47:39 -0500 Subject: [PATCH 28/28] Fix spec example to meet actually behavior. Seems like example was not fully correct. --- SPEC.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/SPEC.md b/SPEC.md index 211955f1..23637a6b 100644 --- a/SPEC.md +++ b/SPEC.md @@ -1819,9 +1819,9 @@ Example output: "c": 12 }, "map_to_struct.map_coercion": { - "beware": 10, - "key": 11, - "lookup": 12 + "a": 10, + "b": 11, + "c": 12 } } ```