stjude-rust-labs/sprocket

wdl-lint: `ShellCheck` should be exceptable on tasks 1 day ago

bug good first issue

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

wdl-lint: split the `RequirementsSection` rule 21 days ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

"Missing version statement" message gaps 28 days ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

stdlib regex functions recompile their pattern on every call 28 days ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

`#@ except: ContainerUri` is not honored on individual `requirements` entries about 1 month ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Add `Diagnostic::help()` getter about 2 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

wdl-lint: `KnownRules` doesn't support trailing commas about 2 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

`dev test`: support `should_fail` on tasks 2 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

wdl-format: extra blank line before workflow `output`/`hints` 3 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

wdl-lsp: bad `parameter_meta` hover docs for objects 3 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Runtime key type checking should be version-aware 3 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

`test` overwhelming the docker daemon 4 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

New `wdl-lint` rule: `PreferStructOverMap` 4 months ago

enhancement good first issue s-blocked

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

feat: better test selection for `test` CLI 4 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

New `wdl-lint` rule: `ModernInterpolation` 4 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

New `wdl-lint` rule: `DenyGlobStar` 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

independently configurable fixtures and run dirs for `test` command 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

format embedded markdown 5 months ago

enhancement help wanted question s-blocked

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

sprocket check/lint runs on files that are in .gitignore 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Lint for tabs in doc comments 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Configurable newline style in `wdl-format` 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

request lint rule: ParameterDescription 5 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

get sprocket format into better shape 6 months ago

enhancement help wanted question

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

lint rule: check object -> struct coercion in declarations 6 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Allow specific additional runtime keys. 6 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

feature request: output directory with symlinks 6 months ago

good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

refactor: move display methods out of `wdl-ast` 6 months ago

enhancement help wanted

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Lint for mixed `meta` sections and doc comments 6 months ago

enhancement good first issue question s-blocked

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

bug: mismatched `meta.outputs` and `outputs` doesn't always result in diagnostics 7 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

TOML errors have poor error reporting 7 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Bad highlights in `lint` 7 months ago

bug good first issue help wanted

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

`validate` does not ensure file existence 8 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

feature request: `wdl-format` should be more opinionated about lint directives 8 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Output total execution time for sprocket run? 8 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

better automatic `.sprocketignore` placement 8 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Sprocket should create ignorefiles for the `runs/` directory 9 months ago

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

bad copy and pastes present in `wdl-lint/rules/` 10 months ago

bug documentation good first issue help wanted

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

docs: the lint rules table has duplicated descriptions 10 months ago

documentation good first issue help wanted

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

request lint rule: ExpectedMetaString 10 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

bug: Bash completions 10 months ago

good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Create a lint for removing unnecessary `input:` prefix when WDL is a high enough version 10 months ago

enhancement good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

bug: `sprocket run` output is missing workflow or task name prefix. about 1 year ago

AI Summary: The task is to fix a bug in the `sprocket run` command where the output JSON is missing the workflow or task name prefix. The issue is identified as a missing call to `outputs.with_name(name)` in the code, which should be a relatively straightforward addition to correct the JSON output to conform to the WDL specification.

Complexity: 2/5

bug good first issue

stjude-rust-labs/sprocket

179

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

Rust

#bioinformatics#bioinformatics-pipeline#wdl#wdl-devtools#wdl-workflow#workflow#workflow-engine

Open Issues Need Help