├── .gitattributes ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report_template.md │ ├── config.yml │ └── feature_request_template.md ├── actions │ └── install-shellcheck │ │ └── action.yaml ├── pull_request_template.md └── workflows │ ├── CI.yml │ ├── bump.yml │ ├── labels.yml │ ├── pr_assign.yml │ ├── release.yml │ └── stale.yml ├── .gitignore ├── .gitmodules ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Cargo.lock ├── Cargo.toml ├── Dockerfile ├── LICENSE-APACHE ├── LICENSE-MIT ├── README.md ├── RELEASE.md ├── assets └── repo-header.png ├── benches ├── analysis │ └── mod.rs ├── bench.rs └── sprocket │ └── mod.rs ├── crates ├── README.md ├── RELEASE.md ├── ci │ ├── Cargo.toml │ └── src │ │ └── main.rs ├── gauntlet │ ├── Arena.toml │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── Gauntlet.toml │ └── src │ │ ├── config.rs │ │ ├── config │ │ └── inner.rs │ │ ├── document.rs │ │ ├── document │ │ └── identifier.rs │ │ ├── lib.rs │ │ ├── main.rs │ │ ├── report.rs │ │ ├── repository.rs │ │ └── repository │ │ ├── identifier.rs │ │ └── work_dir.rs ├── wdl-analysis │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── RULES.md │ ├── src │ │ ├── analyzer.rs │ │ ├── config.rs │ │ ├── diagnostics.rs │ │ ├── document.rs │ │ ├── document │ │ │ └── v1.rs │ │ ├── eval.rs │ │ ├── eval │ │ │ └── v1.rs │ │ ├── graph.rs │ │ ├── handlers.rs │ │ ├── handlers │ │ │ ├── common.rs │ │ │ ├── common │ │ │ │ ├── docs.rs │ │ │ │ └── position.rs │ │ │ ├── completions.rs │ │ │ ├── document_symbol.rs │ │ │ ├── find_all_references.rs │ │ │ ├── goto_definition.rs │ │ │ ├── hover.rs │ │ │ ├── rename.rs │ │ │ ├── semantic_tokens.rs │ │ │ ├── signature_help.rs │ │ │ ├── snippets.rs │ │ │ └── workspace_symbol.rs │ │ ├── lib.rs │ │ ├── queue.rs │ │ ├── rayon.rs │ │ ├── rules.rs │ │ ├── stdlib.rs │ │ ├── stdlib │ │ │ └── constraints.rs │ │ ├── types.rs │ │ ├── types │ │ │ └── v1.rs │ │ ├── validation.rs │ │ ├── validation │ │ │ ├── counts.rs │ │ │ ├── env.rs │ │ │ ├── exprs.rs │ │ │ ├── imports.rs │ │ │ ├── keys.rs │ │ │ ├── numbers.rs │ │ │ ├── requirements.rs │ │ │ ├── strings.rs │ │ │ └── version.rs │ │ └── visitor.rs │ └── tests │ │ ├── analysis.rs │ │ ├── analysis │ │ ├── allow-nested-inputs-1.0 │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── allow-nested-inputs-1.1 │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── allow-nested-inputs-1.2 │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── argument-type-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── array-type-identification │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── braced-command │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── call-input-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── call-multiple-namespaces │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── call-unknown-input │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── call-unknown-task │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── cannot-coerce-string │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── common-types │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── comparison-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conditional-type-mismatch │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-call-names │ │ │ ├── baz.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-decl-names │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-imports │ │ │ ├── Baz │ │ │ ├── Baz.wdl │ │ │ ├── bad-file-name.wdl │ │ │ ├── foo │ │ │ ├── foo.wdl │ │ │ ├── md5sum.wdl │ │ │ ├── qux │ │ │ │ └── baz.wdl │ │ │ ├── source.diagnostics │ │ │ ├── source.wdl │ │ │ └── star.wdl │ │ ├── conflicting-member-names │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-struct-names │ │ │ ├── bar.wdl │ │ │ ├── baz.wdl │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-task-names │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── conflicting-workflow-names │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── duplicate-task │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── env-vars │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── forward-reference │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── hints-section │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── if-conditional-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── ignorefile │ │ │ ├── config.toml │ │ │ ├── malformed_but_ignored.wdl │ │ │ ├── source.diagnostics │ │ │ └── wdlanalysisignore │ │ ├── import-dependency-cycle │ │ │ ├── bar.wdl │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-failed-http │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-incompatible-versions-fallback │ │ │ ├── config.toml │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-incompatible-versions │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-missing-version │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-missing │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-relative │ │ │ ├── a │ │ │ │ └── file.wdl │ │ │ ├── b │ │ │ │ └── file.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-same-struct │ │ │ ├── a │ │ │ │ └── file.wdl │ │ │ ├── b │ │ │ │ └── file.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── import-unsupported-scheme │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── imported-optional-type │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── imported-struct-conflict │ │ │ ├── bar.wdl │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── index-not-integer │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── index-target-not-array │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── inputs-with-none │ │ │ ├── source.diagnostics │ │ │ ├── source.wdl │ │ │ └── w.wdl │ │ ├── invalid-access │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── logical-and-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── logical-not-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── logical-or-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── map-coercions │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── map-key-not-primitive │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── missing-aliased-struct │ │ │ ├── bar.wdl │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── missing-call-input │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── missing-struct-member │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── name-reference-cycle │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── negation-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── non-empty-array │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── not-a-struct-member │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── numeric-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── pair-accessor │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── placeholder-options │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── primitive-type-structs │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── recursive-structs │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── recursive-workflow-call │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── requirements-section │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── runtime-section │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── scatter-not-array │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── self-referential-name │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── static-regex-validation │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-max-retries-not-in-v1-2 │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-command │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-full │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-hints │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-output │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-previous-not-in-v1-2 │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-requirements │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-scope-runtime │ │ │ ├── config.toml │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-variable-unsupported │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── task-variable │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── too-few-arguments │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── too-many-arguments │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── too-many-workflows │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── type-mismatch │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unknown-call-output │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unknown-function │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unknown-name │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unknown-namespace │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unknown-type │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unnecessary-function-calls │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unsupported-function │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unused-call │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unused-decl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unused-file-input │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── unused-import │ │ │ ├── bar.wdl │ │ │ ├── baz.wdl │ │ │ ├── foo.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── workflow-reference-cycle │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ └── workflow │ │ │ ├── other.wdl │ │ │ ├── source.diagnostics │ │ │ └── source.wdl │ │ ├── validation.rs │ │ └── validation │ │ ├── conflicting-sections │ │ ├── source.errors │ │ └── source.wdl │ │ ├── directory-type-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── directory-type │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-call-inputs │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-command │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-hints │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-input │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-output │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-param-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-placeholder-options │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-requirements │ │ ├── source.errors │ │ └── source.wdl │ │ ├── duplicate-runtime │ │ ├── source.errors │ │ └── source.wdl │ │ ├── else-if-wdl-1-2 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── else-if-wdl-1-3 │ │ ├── config.toml │ │ ├── source.errors │ │ └── source.wdl │ │ ├── empty-struct │ │ ├── source.errors │ │ └── source.wdl │ │ ├── empty │ │ ├── source.errors │ │ └── source.wdl │ │ ├── env-vars-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── env-vars │ │ ├── source.errors │ │ └── source.wdl │ │ ├── exponentiation-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── float-out-of-range │ │ ├── source.errors │ │ └── source.wdl │ │ ├── hints-conflicting-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── hints-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── hints-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── hints │ │ ├── source.errors │ │ └── source.wdl │ │ ├── import-namespace-invalid │ │ ├── invalid-namespace.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── int-out-of-range │ │ ├── source.errors │ │ └── source.wdl │ │ ├── invalid-use-type │ │ ├── source.errors │ │ └── source.wdl │ │ ├── literal-object-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── literal-struct-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── metadata-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── metadata-object-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-call-input-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-call-input │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-command-section │ │ ├── source.errors │ │ └── source.wdl │ │ ├── multiline-strings-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── multiline-strings │ │ ├── source.errors │ │ └── source.wdl │ │ ├── param-metadata-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── placeholder-in-import │ │ ├── ok.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── requirements-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── requirements-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── requirements-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-duplicate-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── scoped-exprs │ │ ├── source.errors │ │ └── source.wdl │ │ ├── single-struct │ │ ├── source.errors │ │ └── source.wdl │ │ ├── single-task │ │ ├── source.errors │ │ └── source.wdl │ │ ├── single-workflow │ │ ├── source.errors │ │ └── source.wdl │ │ ├── strings │ │ ├── source.errors │ │ └── source.wdl │ │ ├── struct-metadata-unsupported │ │ ├── source.errors │ │ └── source.wdl │ │ ├── struct-metadata │ │ ├── source.errors │ │ └── source.wdl │ │ ├── unsupported-version-fallback-suppress-warning │ │ ├── config.toml │ │ ├── source.errors │ │ └── source.wdl │ │ ├── unsupported-version-fallback │ │ ├── config.toml │ │ ├── source.errors │ │ └── source.wdl │ │ └── unsupported-version │ │ ├── source.errors │ │ └── source.wdl ├── wdl-ast │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── src │ │ ├── element.rs │ │ ├── lib.rs │ │ ├── v1.rs │ │ └── v1 │ │ │ ├── decls.rs │ │ │ ├── display.rs │ │ │ ├── expr.rs │ │ │ ├── import.rs │ │ │ ├── struct.rs │ │ │ ├── task.rs │ │ │ ├── task │ │ │ ├── common.rs │ │ │ ├── common │ │ │ │ ├── container.rs │ │ │ │ └── container │ │ │ │ │ ├── value.rs │ │ │ │ │ └── value │ │ │ │ │ └── uri.rs │ │ │ ├── requirements.rs │ │ │ ├── requirements │ │ │ │ ├── item.rs │ │ │ │ └── item │ │ │ │ │ └── container.rs │ │ │ ├── runtime.rs │ │ │ └── runtime │ │ │ │ ├── item.rs │ │ │ │ └── item │ │ │ │ └── container.rs │ │ │ ├── tokens.rs │ │ │ └── workflow.rs │ └── tests │ │ └── registry.rs ├── wdl-doc │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── build.rs │ ├── src │ │ ├── command_section.rs │ │ ├── docs_tree.rs │ │ ├── document.rs │ │ ├── lib.rs │ │ ├── meta.rs │ │ ├── parameter.rs │ │ ├── runnable.rs │ │ ├── runnable │ │ │ ├── task.rs │ │ │ └── workflow.rs │ │ └── struct.rs │ ├── tests │ │ ├── codebase │ │ │ ├── data_structures │ │ │ │ ├── flag_filter.wdl │ │ │ │ └── read_group.wdl │ │ │ └── docs │ │ │ │ ├── assets │ │ │ │ ├── category-selected.light.svg │ │ │ │ ├── category-selected.svg │ │ │ │ ├── category-unselected.light.svg │ │ │ │ ├── category-unselected.svg │ │ │ │ ├── chevron-down.light.svg │ │ │ │ ├── chevron-down.svg │ │ │ │ ├── chevron-up.light.svg │ │ │ │ ├── chevron-up.svg │ │ │ │ ├── dir-open.light.svg │ │ │ │ ├── dir-open.svg │ │ │ │ ├── folder-selected.light.svg │ │ │ │ ├── folder-selected.svg │ │ │ │ ├── folder-unselected.light.svg │ │ │ │ ├── folder-unselected.svg │ │ │ │ ├── information-circle.light.svg │ │ │ │ ├── information-circle.svg │ │ │ │ ├── link.light.svg │ │ │ │ ├── link.svg │ │ │ │ ├── list-bullet-selected.light.svg │ │ │ │ ├── list-bullet-selected.svg │ │ │ │ ├── list-bullet-unselected.light.svg │ │ │ │ ├── list-bullet-unselected.svg │ │ │ │ ├── logo.light.svg │ │ │ │ ├── logo.svg │ │ │ │ ├── missing-home.light.svg │ │ │ │ ├── missing-home.svg │ │ │ │ ├── search.light.svg │ │ │ │ ├── search.svg │ │ │ │ ├── sidebar-icon-default.light.svg │ │ │ │ ├── sidebar-icon-default.svg │ │ │ │ ├── sidebar-icon-expand.light.svg │ │ │ │ ├── sidebar-icon-expand.svg │ │ │ │ ├── sidebar-icon-hide.light.svg │ │ │ │ ├── sidebar-icon-hide.svg │ │ │ │ ├── struct-selected.light.svg │ │ │ │ ├── struct-selected.svg │ │ │ │ ├── struct-unselected.light.svg │ │ │ │ ├── struct-unselected.svg │ │ │ │ ├── task-selected.light.svg │ │ │ │ ├── task-selected.svg │ │ │ │ ├── task-unselected.light.svg │ │ │ │ ├── task-unselected.svg │ │ │ │ ├── wdl-dir-selected.light.svg │ │ │ │ ├── wdl-dir-selected.svg │ │ │ │ ├── wdl-dir-unselected.light.svg │ │ │ │ ├── wdl-dir-unselected.svg │ │ │ │ ├── workflow-selected.light.svg │ │ │ │ ├── workflow-selected.svg │ │ │ │ ├── workflow-unselected.light.svg │ │ │ │ ├── workflow-unselected.svg │ │ │ │ ├── x-mark.light.svg │ │ │ │ └── x-mark.svg │ │ │ │ ├── data_structures │ │ │ │ ├── flag_filter │ │ │ │ │ ├── FlagFilter-struct.html │ │ │ │ │ ├── index.html │ │ │ │ │ ├── validate_flag_filter-workflow.html │ │ │ │ │ └── validate_string_is_12bit_oct_dec_or_hex-task.html │ │ │ │ └── read_group │ │ │ │ │ ├── ReadGroup-struct.html │ │ │ │ │ ├── get_read_groups-task.html │ │ │ │ │ ├── index.html │ │ │ │ │ ├── read_group_to_string-task.html │ │ │ │ │ └── validate_read_group-task.html │ │ │ │ ├── index.html │ │ │ │ ├── index.js │ │ │ │ └── style.css │ │ ├── doc.rs │ │ └── output_docs │ │ │ ├── assets │ │ │ ├── category-selected.light.svg │ │ │ ├── category-selected.svg │ │ │ ├── category-unselected.light.svg │ │ │ ├── category-unselected.svg │ │ │ ├── chevron-down.light.svg │ │ │ ├── chevron-down.svg │ │ │ ├── chevron-up.light.svg │ │ │ ├── chevron-up.svg │ │ │ ├── dir-open.light.svg │ │ │ ├── dir-open.svg │ │ │ ├── folder-selected.light.svg │ │ │ ├── folder-selected.svg │ │ │ ├── folder-unselected.light.svg │ │ │ ├── folder-unselected.svg │ │ │ ├── information-circle.light.svg │ │ │ ├── information-circle.svg │ │ │ ├── link.light.svg │ │ │ ├── link.svg │ │ │ ├── list-bullet-selected.light.svg │ │ │ ├── list-bullet-selected.svg │ │ │ ├── list-bullet-unselected.light.svg │ │ │ ├── list-bullet-unselected.svg │ │ │ ├── logo.light.svg │ │ │ ├── logo.svg │ │ │ ├── missing-home.light.svg │ │ │ ├── missing-home.svg │ │ │ ├── search.light.svg │ │ │ ├── search.svg │ │ │ ├── sidebar-icon-default.light.svg │ │ │ ├── sidebar-icon-default.svg │ │ │ ├── sidebar-icon-expand.light.svg │ │ │ ├── sidebar-icon-expand.svg │ │ │ ├── sidebar-icon-hide.light.svg │ │ │ ├── sidebar-icon-hide.svg │ │ │ ├── struct-selected.light.svg │ │ │ ├── struct-selected.svg │ │ │ ├── struct-unselected.light.svg │ │ │ ├── struct-unselected.svg │ │ │ ├── task-selected.light.svg │ │ │ ├── task-selected.svg │ │ │ ├── task-unselected.light.svg │ │ │ ├── task-unselected.svg │ │ │ ├── wdl-dir-selected.light.svg │ │ │ ├── wdl-dir-selected.svg │ │ │ ├── wdl-dir-unselected.light.svg │ │ │ ├── wdl-dir-unselected.svg │ │ │ ├── workflow-selected.light.svg │ │ │ ├── workflow-selected.svg │ │ │ ├── workflow-unselected.light.svg │ │ │ ├── workflow-unselected.svg │ │ │ ├── x-mark.light.svg │ │ │ └── x-mark.svg │ │ │ ├── data_structures │ │ │ ├── flag_filter │ │ │ │ ├── FlagFilter-struct.html │ │ │ │ ├── index.html │ │ │ │ ├── validate_flag_filter-workflow.html │ │ │ │ └── validate_string_is_12bit_oct_dec_or_hex-task.html │ │ │ └── read_group │ │ │ │ ├── ReadGroup-struct.html │ │ │ │ ├── get_read_groups-task.html │ │ │ │ ├── index.html │ │ │ │ ├── read_group_to_string-task.html │ │ │ │ └── validate_read_group-task.html │ │ │ ├── index.html │ │ │ ├── index.js │ │ │ └── style.css │ └── theme │ │ ├── assets │ │ ├── category-selected.light.svg │ │ ├── category-selected.svg │ │ ├── category-unselected.light.svg │ │ ├── category-unselected.svg │ │ ├── chevron-down.light.svg │ │ ├── chevron-down.svg │ │ ├── chevron-up.light.svg │ │ ├── chevron-up.svg │ │ ├── dir-open.light.svg │ │ ├── dir-open.svg │ │ ├── folder-selected.light.svg │ │ ├── folder-selected.svg │ │ ├── folder-unselected.light.svg │ │ ├── folder-unselected.svg │ │ ├── information-circle.light.svg │ │ ├── information-circle.svg │ │ ├── link.light.svg │ │ ├── link.svg │ │ ├── list-bullet-selected.light.svg │ │ ├── list-bullet-selected.svg │ │ ├── list-bullet-unselected.light.svg │ │ ├── list-bullet-unselected.svg │ │ ├── logo.light.svg │ │ ├── logo.svg │ │ ├── missing-home.light.svg │ │ ├── missing-home.svg │ │ ├── search.light.svg │ │ ├── search.svg │ │ ├── sidebar-icon-default.light.svg │ │ ├── sidebar-icon-default.svg │ │ ├── sidebar-icon-expand.light.svg │ │ ├── sidebar-icon-expand.svg │ │ ├── sidebar-icon-hide.light.svg │ │ ├── sidebar-icon-hide.svg │ │ ├── struct-selected.light.svg │ │ ├── struct-selected.svg │ │ ├── struct-unselected.light.svg │ │ ├── struct-unselected.svg │ │ ├── task-selected.light.svg │ │ ├── task-selected.svg │ │ ├── task-unselected.light.svg │ │ ├── task-unselected.svg │ │ ├── wdl-dir-selected.light.svg │ │ ├── wdl-dir-selected.svg │ │ ├── wdl-dir-unselected.light.svg │ │ ├── wdl-dir-unselected.svg │ │ ├── workflow-selected.light.svg │ │ ├── workflow-selected.svg │ │ ├── workflow-unselected.light.svg │ │ ├── workflow-unselected.svg │ │ ├── x-mark.light.svg │ │ └── x-mark.svg │ │ ├── dist │ │ ├── index.js │ │ └── style.css │ │ ├── package-lock.json │ │ ├── package.json │ │ ├── postcss.config.js │ │ ├── src │ │ ├── colors.css │ │ ├── main.css │ │ └── markdown.css │ │ ├── tailwind.config.js │ │ └── web-components │ │ ├── index.js │ │ ├── sprocket-code.js │ │ ├── sprocket-code.utils.js │ │ └── sprocket-tooltip.js ├── wdl-engine │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── src │ │ ├── backend.rs │ │ ├── backend │ │ │ ├── apptainer.rs │ │ │ ├── apptainer │ │ │ │ └── images.rs │ │ │ ├── docker.rs │ │ │ ├── local.rs │ │ │ ├── lsf_apptainer.rs │ │ │ ├── slurm_apptainer.rs │ │ │ └── tes.rs │ │ ├── cache.rs │ │ ├── cache │ │ │ ├── hash.rs │ │ │ └── lock.rs │ │ ├── config.rs │ │ ├── diagnostics.rs │ │ ├── digest.rs │ │ ├── eval.rs │ │ ├── eval │ │ │ ├── trie.rs │ │ │ ├── v1.rs │ │ │ └── v1 │ │ │ │ ├── expr.rs │ │ │ │ ├── task.rs │ │ │ │ ├── validators.rs │ │ │ │ └── workflow.rs │ │ ├── http.rs │ │ ├── inputs.rs │ │ ├── lib.rs │ │ ├── outputs.rs │ │ ├── path.rs │ │ ├── stdlib.rs │ │ ├── stdlib │ │ │ ├── as_map.rs │ │ │ ├── as_pairs.rs │ │ │ ├── basename.rs │ │ │ ├── ceil.rs │ │ │ ├── chunk.rs │ │ │ ├── collect_by_key.rs │ │ │ ├── contains.rs │ │ │ ├── contains_key.rs │ │ │ ├── cross.rs │ │ │ ├── defined.rs │ │ │ ├── find.rs │ │ │ ├── flatten.rs │ │ │ ├── floor.rs │ │ │ ├── glob.rs │ │ │ ├── join_paths.rs │ │ │ ├── keys.rs │ │ │ ├── length.rs │ │ │ ├── matches.rs │ │ │ ├── max.rs │ │ │ ├── min.rs │ │ │ ├── prefix.rs │ │ │ ├── quote.rs │ │ │ ├── range.rs │ │ │ ├── read_boolean.rs │ │ │ ├── read_float.rs │ │ │ ├── read_int.rs │ │ │ ├── read_json.rs │ │ │ ├── read_lines.rs │ │ │ ├── read_map.rs │ │ │ ├── read_object.rs │ │ │ ├── read_objects.rs │ │ │ ├── read_string.rs │ │ │ ├── read_tsv.rs │ │ │ ├── round.rs │ │ │ ├── select_all.rs │ │ │ ├── select_first.rs │ │ │ ├── sep.rs │ │ │ ├── size.rs │ │ │ ├── split.rs │ │ │ ├── squote.rs │ │ │ ├── stderr.rs │ │ │ ├── stdout.rs │ │ │ ├── sub.rs │ │ │ ├── suffix.rs │ │ │ ├── transpose.rs │ │ │ ├── unzip.rs │ │ │ ├── values.rs │ │ │ ├── write_json.rs │ │ │ ├── write_lines.rs │ │ │ ├── write_map.rs │ │ │ ├── write_object.rs │ │ │ ├── write_objects.rs │ │ │ ├── write_tsv.rs │ │ │ └── zip.rs │ │ ├── tree.rs │ │ ├── units.rs │ │ └── value.rs │ └── tests │ │ ├── common │ │ └── mod.rs │ │ ├── inputs.rs │ │ ├── inputs │ │ ├── call-input-present │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── coerce-to-string │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── complex-types │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── default-workflow-inputs │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── empty │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── explicit-nested-inputs-not-allowed │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── invalid-hints-type │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── invalid-requirement-type │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── invalid-runtime-type │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── invalid-wdl-array │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── known-requirement │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── missing-call-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── missing-file │ │ │ ├── error.txt │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── missing-prefix │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── missing-task-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── missing-workflow-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── mixed-prefixes │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── nested-input-already-specified │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── nested-inputs-not-allowed │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-call-1_2 │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-call │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-hint │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-nested-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-requirement │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-task-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── unknown-task-or-workflow │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ └── unknown-workflow-input │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── inputs.yaml │ │ │ └── source.wdl │ │ ├── tasks.rs │ │ ├── tasks │ │ ├── array-access │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── array-map-equality │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── change-extension-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── foo.data │ │ │ │ └── foo.index │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── clobber │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── foo.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── compare-coerced │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── compare-optionals │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── concat-optional │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── cpu_limit │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── error.txt │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── declarations │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── default-option-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── result1 │ │ │ │ ├── result2 │ │ │ │ └── result3 │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── env_var_guest_path │ │ │ ├── command │ │ │ ├── foo.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── expressions-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── hello.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── file-output-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── foo.goodbye │ │ │ │ └── foo.hello │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── file-sizes-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── created_file │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── file-sizes │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── created_file │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── flags-task │ │ │ ├── command │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── funky-input-filename │ │ │ ├── command │ │ │ ├── greetings (final) (2).txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── glob-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── file_1.txt │ │ │ │ ├── file_2.txt │ │ │ │ └── file_3.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── hello │ │ │ ├── command │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── if-type-mismatch │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ └── source.wdl │ │ ├── import-structs │ │ │ ├── command │ │ │ ├── hello.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── input-path-mapping │ │ │ ├── a.txt │ │ │ ├── b.txt │ │ │ ├── c.txt │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── input-type-qualifiers │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── result │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── invalid-placeholder-default │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ └── source.wdl │ │ ├── invalid-placeholder-sep │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ └── source.wdl │ │ ├── invalid-placeholder-true-false │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ └── source.wdl │ │ ├── member-access │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── memory_limit │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── error.txt │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── missing-output-file │ │ │ ├── command │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multiline-placeholders │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multiline-strings1 │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multiline-strings2 │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multiline-strings3 │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multiline-strings4 │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── nested-access │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── nested-placeholders │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── non-empty-optional │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── optional-output-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── example1.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── optionals │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── outputs-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── a.csv │ │ │ │ ├── b.csv │ │ │ │ └── threshold.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── override_cpu_limit │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── override_memory_limit │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── path-translation │ │ │ ├── a.txt │ │ │ ├── b.txt │ │ │ ├── c.txt │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── person-struct-task │ │ │ ├── command │ │ │ ├── hello.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── placeholder-coercion │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── placeholder-none │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── placeholders │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── primitive-literals │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── testdir │ │ │ │ │ └── hello.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── primitive-to-string │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── private-declaration-task │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── relative-and-absolute-task │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── my │ │ │ │ │ └── path │ │ │ │ │ └── to │ │ │ │ │ └── something.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── retry │ │ │ ├── command │ │ │ ├── files │ │ │ │ └── done.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── sep-option-to-function │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── split-task │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── files │ │ │ │ └── file.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── string-to-file │ │ │ ├── command │ │ │ ├── data │ │ │ │ └── file │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── struct-to-struct │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── sum-task │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-fail │ │ │ ├── command │ │ │ ├── error.txt │ │ │ ├── inputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-inputs-task │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-retry-with-memory-increase │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-scope-command │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-scope-output │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-scope-requirements │ │ │ ├── command │ │ │ ├── config-override.yaml │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-variable │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── task-with-comments │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── ternary │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-basename │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-ceil │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-find │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-floor │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-join-paths │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── mydata.txt │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-map │ │ │ ├── command │ │ │ ├── data │ │ │ │ ├── file1 │ │ │ │ └── file2 │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-matches │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── sample1234_R1.fastq │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-max │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-min │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-object │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-pairs │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-placeholders-task │ │ │ ├── command │ │ │ ├── greetings.txt │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-round │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-stderr │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-stdout │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-struct │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── test-sub │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── true-false-ternary │ │ │ ├── command │ │ │ ├── files │ │ │ │ ├── result1 │ │ │ │ └── result2 │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── unclean-input-path │ │ │ ├── command │ │ │ ├── inputs.json │ │ │ ├── message.txt │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ └── work-dir-perms │ │ │ ├── command │ │ │ ├── files │ │ │ └── foo │ │ │ ├── inputs.json │ │ │ ├── outputs.json │ │ │ ├── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── workflows.rs │ │ └── workflows │ │ ├── allow-nested │ │ ├── hello.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── array-access │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── array-literal-coersion │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── array-map-equality │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── as-map │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── call-example │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── call-imported-task │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── callstack │ │ ├── error.txt │ │ ├── first.wdl │ │ ├── inputs.json │ │ ├── second.wdl │ │ └── source.wdl │ │ ├── compare-coerced │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── compare-optionals │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── concat-optional │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── concurrent-localization │ │ ├── inputs.json │ │ ├── local.txt │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── copy-inputs │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── declarations │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── empty-array-fail │ │ ├── error.txt │ │ ├── inputs.json │ │ └── source.wdl │ │ ├── env-vars │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── example-ternary │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── hello-parallel │ │ ├── greetings.txt │ │ ├── hello.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── hello │ │ ├── greetings.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── if-else │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── if-expr-array │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── illegal-access │ │ ├── error.txt │ │ ├── inputs.json │ │ └── source.wdl │ │ ├── import-structs │ │ ├── hello.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── input-ref-call │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── inputs-with-none │ │ ├── inputs.json │ │ ├── outputs.json │ │ ├── source.wdl │ │ └── w.wdl │ │ ├── localization │ │ ├── foo.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── map-literal-coercion │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── map-to-array │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── map-to-struct │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── member-access │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multi-nested-inputs │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multiline-string-placeholders │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multiline-strings │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multiline-strings2 │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multiline-strings3 │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── multiline-strings4 │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── nested-access │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── nested-if │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── nested-placeholders │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── nested-scatter │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── non-empty-array-fail │ │ ├── error.txt │ │ ├── inputs.json │ │ └── source.wdl │ │ ├── non-empty-optional │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── optional-with-defaults │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── optionals │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── pair-to-array │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── pair-to-struct │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── placeholder-none │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── placeholders-coercion │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── placeholders │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── primitive-literals │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── primitive-to-string │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── read-remote-file │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── scatter-array-type │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── sep-option-to-function │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── serde-pair │ │ ├── cities.txt │ │ ├── hello.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── string-to-file │ │ ├── data │ │ │ └── file │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── struct-to-struct │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── task-outputs │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-after │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-allow-nested-inputs │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-conditional │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-containers │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-fully-qualified-names │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-input-keyword │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-local-call │ │ ├── greetings.txt │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-map-fail │ │ ├── error.txt │ │ ├── inputs.json │ │ └── source.wdl │ │ ├── test-map-ordering │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-maps │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-meta-values │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-object │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-pairs │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-scatter │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ ├── test-struct │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl │ │ └── workflow-with-comments │ │ ├── inputs.json │ │ ├── outputs.json │ │ └── source.wdl ├── wdl-format │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── src │ │ ├── config.rs │ │ ├── config │ │ │ ├── builder.rs │ │ │ ├── indent.rs │ │ │ └── max_line_length.rs │ │ ├── element.rs │ │ ├── element │ │ │ └── node.rs │ │ ├── lib.rs │ │ ├── token.rs │ │ ├── token │ │ │ ├── post.rs │ │ │ └── pre.rs │ │ ├── v1.rs │ │ └── v1 │ │ │ ├── decl.rs │ │ │ ├── expr.rs │ │ │ ├── import.rs │ │ │ ├── meta.rs │ │ │ ├── sort.rs │ │ │ ├── struct.rs │ │ │ ├── task.rs │ │ │ ├── workflow.rs │ │ │ └── workflow │ │ │ └── call.rs │ └── tests │ │ ├── format.rs │ │ └── format │ │ ├── ENCODE-DCC_chip-seq-pipeline │ │ ├── LICENSE.txt │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── clays_complex_script │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── complex_meta_and_calls │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── env-vars │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── funky_command_leading_whitespace │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── if_then_else_exprs │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── imports_with_both_comments │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── imports_with_inline_comments │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── imports_with_no_comments │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── imports_with_preceding_comments │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── interrupt_example │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── issue-289 │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── multiline-strings │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── not_covered_by_other_tests │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── optional_structs │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── seaseq-case │ │ ├── LICENSE.txt │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── sort-inputs │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── string-escaping │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ ├── trailing-trivia │ │ ├── source.formatted.wdl │ │ └── source.wdl │ │ └── tricky-trailing-trivia │ │ ├── source.formatted.wdl │ │ └── source.wdl ├── wdl-grammar │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── src │ │ ├── diagnostic.rs │ │ ├── grammar.rs │ │ ├── grammar │ │ │ └── v1.rs │ │ ├── lexer.rs │ │ ├── lexer │ │ │ └── v1.rs │ │ ├── lib.rs │ │ ├── parser.rs │ │ ├── tree.rs │ │ ├── tree │ │ │ └── dive.rs │ │ └── version.rs │ └── tests │ │ ├── parsing.rs │ │ └── parsing │ │ ├── atoms │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── brace-command-recovery │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── call-statements │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── command-sections │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── conditional-statements │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── consistent-comments │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-array-type │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-call │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-conditional │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-document │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-index-expr │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-map-type │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-pair-type │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── empty-scatter │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── env-vars │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── escaped-newlines │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── exponentiation │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── hints-section │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── if-then-else-expr │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── if-then-else │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── imports │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── infix-exprs │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── input-sections │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── interpolation │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── long-call-target │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── metadata-recovery │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── metadata │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── mismatched-brace │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── mismatched-bracket │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── missing-brace │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── missing-comma │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── missing-version │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── multiline-strings │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── multiple-placeholder-opts │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── name-ref │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── optional-call-input │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── output-sections │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── placeholder-in-metadata │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── postfix-exprs │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── precedence │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── prefix-exprs │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── recovery-past-string │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── requirements-section │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── reserved-meta-names │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── runtime-sections │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── scatter-statements │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── struct-definitions │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── struct-literal-with-string │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── struct-meta │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── struct-recovery │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── top-recovery │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── unbound-decl-in-output │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── unexpected-string │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── unterminated-metadata-string │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ ├── version-invalid │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl │ │ └── version-valid │ │ ├── source.errors │ │ ├── source.tree │ │ └── source.wdl ├── wdl-lint │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── DEFINITIONS.md │ ├── RULES.md │ ├── src │ │ ├── fix.rs │ │ ├── lib.rs │ │ ├── linter.rs │ │ ├── rules.rs │ │ ├── rules │ │ │ ├── call_input_keyword.rs │ │ │ ├── call_input_spacing.rs │ │ │ ├── command_section_indentation.rs │ │ │ ├── comment_whitespace.rs │ │ │ ├── concise_input.rs │ │ │ ├── consistent_newlines.rs │ │ │ ├── container_uri.rs │ │ │ ├── declaration_name.rs │ │ │ ├── deprecated_object.rs │ │ │ ├── deprecated_placeholder.rs │ │ │ ├── description_length.rs │ │ │ ├── doc_meta_strings.rs │ │ │ ├── double_quotes.rs │ │ │ ├── element_spacing.rs │ │ │ ├── ending_newline.rs │ │ │ ├── expected_runtime_keys.rs │ │ │ ├── expression_spacing.rs │ │ │ ├── heredoc_commands.rs │ │ │ ├── import_placement.rs │ │ │ ├── import_sorted.rs │ │ │ ├── import_whitespace.rs │ │ │ ├── input_name.rs │ │ │ ├── input_sorted.rs │ │ │ ├── known_rules.rs │ │ │ ├── line_width.rs │ │ │ ├── lint_directive_formatted.rs │ │ │ ├── lint_directive_valid.rs │ │ │ ├── matching_output_meta.rs │ │ │ ├── meta_description.rs │ │ │ ├── meta_key_value_formatting.rs │ │ │ ├── meta_sections.rs │ │ │ ├── output_name.rs │ │ │ ├── parameter_meta_matched.rs │ │ │ ├── pascal_case.rs │ │ │ ├── preamble_comment_placement.rs │ │ │ ├── preamble_formatted.rs │ │ │ ├── redundant_none.rs │ │ │ ├── requirements_section.rs │ │ │ ├── runtime_section.rs │ │ │ ├── section_order.rs │ │ │ ├── shellcheck.rs │ │ │ ├── snake_case.rs │ │ │ ├── todo_comment.rs │ │ │ ├── trailing_comma.rs │ │ │ ├── version_statement_formatted.rs │ │ │ └── whitespace.rs │ │ ├── tags.rs │ │ └── util.rs │ └── tests │ │ ├── lints.rs │ │ └── lints │ │ ├── alternate-preamble-directive-comments │ │ ├── source.errors │ │ └── source.wdl │ │ ├── between-import-whitespace │ │ ├── bar.wdl │ │ ├── baz.wdl │ │ ├── foo.wdl │ │ ├── huh.wdl │ │ ├── source.errors │ │ ├── source.wdl │ │ ├── vom.wdl │ │ ├── wah.wdl │ │ └── zam.wdl │ │ ├── blank-lines-between-elements │ │ ├── baz.wdl │ │ ├── qux.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── call-input-keyword-v1-1 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── call-input-keyword │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-line-cont │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-same-line │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-spaces-first │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-tabs-first │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-trailing │ │ ├── source.errors │ │ └── source.wdl │ │ ├── command-mixed-ws-ok │ │ ├── source.errors │ │ └── source.wdl │ │ ├── comment-whitespace │ │ ├── source.errors │ │ └── source.wdl │ │ ├── container-value │ │ ├── source.errors │ │ └── source.wdl │ │ ├── curly-command │ │ ├── source.errors │ │ └── source.wdl │ │ ├── deprecated-object │ │ ├── source.errors │ │ └── source.wdl │ │ ├── deprecated-placeholder-options-v1.0 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── deprecated-placeholder-options-v1.1 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── description-missing │ │ ├── source.errors │ │ └── source.wdl │ │ ├── description-too-long │ │ ├── source.errors │ │ └── source.wdl │ │ ├── disallowed-declaration-name │ │ ├── source.errors │ │ └── source.wdl │ │ ├── disallowed-input-name │ │ ├── source.errors │ │ └── source.wdl │ │ ├── disallowed-output-name │ │ ├── source.errors │ │ └── source.wdl │ │ ├── doc-meta-strings │ │ ├── source.errors │ │ └── source.wdl │ │ ├── double-quotes │ │ ├── source.errors │ │ └── source.wdl │ │ ├── except │ │ ├── source.errors │ │ └── source.wdl │ │ ├── expression-spacing │ │ ├── source.errors │ │ └── source.wdl │ │ ├── import-placements │ │ ├── bar.wdl │ │ ├── baz.wdl │ │ ├── foo.wdl │ │ ├── jam.wdl │ │ ├── qux.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── import-sorting │ │ ├── A.wdl │ │ ├── B.wdl │ │ ├── C.wdl │ │ ├── D.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── inconsistent-newlines │ │ ├── source.errors │ │ └── source.wdl │ │ ├── input-and-parameter-meta-sorting │ │ ├── source.errors │ │ └── source.wdl │ │ ├── input-not-sorted │ │ ├── source.errors │ │ └── source.wdl │ │ ├── input-spacing │ │ ├── source.errors │ │ └── source.wdl │ │ ├── invalid-preamble-comment │ │ ├── source.errors │ │ └── source.wdl │ │ ├── key-value-pairs │ │ ├── source.errors │ │ └── source.wdl │ │ ├── line-width │ │ ├── source.errors │ │ └── source.wdl │ │ ├── malformed-lint-directive │ │ ├── source.errors │ │ └── source.wdl │ │ ├── matching-param-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-blank-line-after-version │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-comment-space │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-eof-newline │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-meta-and-parameter_meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-parameter_meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-preamble-ws │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-requirements-block │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-runtime-block │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-struct-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── missing-struct-param-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── multiple-eof-newline │ │ ├── source.errors │ │ └── source.wdl │ │ ├── nonmatching-output │ │ ├── source.errors │ │ └── source.wdl │ │ ├── one-eof-newline │ │ ├── source.errors │ │ └── source.wdl │ │ ├── one-invalid-preamble-comment │ │ ├── source.errors │ │ └── source.wdl │ │ ├── one-line-after-version │ │ ├── source.errors │ │ └── source.wdl │ │ ├── only-whitespace │ │ ├── source.errors │ │ └── source.wdl │ │ ├── pascal-case │ │ ├── source.errors │ │ └── source.wdl │ │ ├── preamble-comment-after-version │ │ ├── source.errors │ │ └── source.wdl │ │ ├── preamble-ws │ │ ├── source.errors │ │ └── source.wdl │ │ ├── redundant-assignment │ │ ├── source.errors │ │ └── source.wdl │ │ ├── redundant-input-assignment-wdl-1.0 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── redundant-input-assignment-wdl-1.1 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── redundant-input-assignment-wdl-1.2 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-keys-engine-keys │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-keys-multiple-runtime-sections │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-keys-wdl-1.0 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-keys-wdl-1.1 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── runtime-keys-wdl-1.2 │ │ ├── source.errors │ │ └── source.wdl │ │ ├── section-ordering │ │ ├── source.errors │ │ └── source.wdl │ │ ├── shellcheck-error │ │ ├── source.errors │ │ └── source.wdl │ │ ├── shellcheck-ok │ │ ├── source.errors │ │ └── source.wdl │ │ ├── shellcheck-style │ │ ├── source.errors │ │ └── source.wdl │ │ ├── shellcheck-warn │ │ ├── source.errors │ │ └── source.wdl │ │ ├── snake-case │ │ ├── source.errors │ │ └── source.wdl │ │ ├── struct-matching-param-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── struct-missing-both-meta │ │ ├── source.errors │ │ └── source.wdl │ │ ├── todo │ │ ├── source.errors │ │ └── source.wdl │ │ ├── too-many-pounds-preamble │ │ ├── source.errors │ │ └── source.wdl │ │ ├── trailing-comma │ │ ├── source.errors │ │ └── source.wdl │ │ ├── trailing-comment-whitespace │ │ ├── source.errors │ │ └── source.wdl │ │ ├── two-eof-newline │ │ ├── source.errors │ │ └── source.wdl │ │ ├── unknown_rule │ │ ├── source.errors │ │ └── source.wdl │ │ ├── unnecessary-preamble-ws │ │ ├── source.errors │ │ └── source.wdl │ │ ├── within-import-whitespace │ │ ├── bar.wdl │ │ ├── baz.wdl │ │ ├── chuk.wdl │ │ ├── corge.wdl │ │ ├── foo.wdl │ │ ├── lorem.wdl │ │ ├── qux.wdl │ │ ├── source.errors │ │ └── source.wdl │ │ ├── ws-before-version │ │ ├── source.errors │ │ └── source.wdl │ │ └── ws-preamble-comments │ │ ├── source.errors │ │ └── source.wdl ├── wdl-lsp │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── src │ │ ├── lib.rs │ │ ├── proto.rs │ │ └── server.rs │ └── tests │ │ ├── common.rs │ │ ├── completions.rs │ │ ├── find_all_references.rs │ │ ├── goto_definition.rs │ │ ├── hover.rs │ │ ├── rename.rs │ │ ├── signature_help.rs │ │ ├── symbols.rs │ │ └── workspace │ │ ├── completions │ │ ├── lib.wdl │ │ ├── namespaces.wdl │ │ ├── partial.wdl │ │ ├── scopes.wdl │ │ ├── sections.wdl │ │ ├── snippet_keyword.wdl │ │ ├── snippet_local.wdl │ │ ├── snippet_ns.wdl │ │ ├── snippet_struct.wdl │ │ ├── source.wdl │ │ ├── taskvar.wdl │ │ └── version.wdl │ │ ├── find_references │ │ ├── foo.wdl │ │ ├── source.wdl │ │ └── structs.wdl │ │ ├── goto_definition │ │ ├── lib.wdl │ │ ├── source.wdl │ │ └── structs.wdl │ │ ├── hover │ │ ├── lib.wdl │ │ ├── meta.wdl │ │ └── source.wdl │ │ ├── rename │ │ ├── foo.wdl │ │ ├── shadowed.wdl │ │ ├── source.wdl │ │ └── structs.wdl │ │ ├── signature_help │ │ └── source.wdl │ │ └── symbols │ │ ├── lib.wdl │ │ └── source.wdl └── wdl │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── examples │ ├── explore.rs │ └── parse.rs │ └── src │ └── lib.rs ├── deny.toml ├── rustfmt.toml ├── src ├── analysis.rs ├── analysis │ ├── results.rs │ └── source.rs ├── commands.rs ├── commands │ ├── analyzer.rs │ ├── check.rs │ ├── completions.rs │ ├── config.rs │ ├── doc.rs │ ├── explain.rs │ ├── format.rs │ ├── inputs.rs │ ├── lock.rs │ ├── run.rs │ ├── test.rs │ └── validate.rs ├── config.rs ├── diagnostics.rs ├── eval.rs ├── inputs.rs ├── inputs │ ├── file.rs │ └── origin_paths.rs ├── lib.rs ├── main.rs ├── memory_stats.rs └── test.rs ├── test-configs ├── lsf-apptainer-engine.toml └── slurm-apptainer-engine.toml ├── tests ├── cli.rs ├── cli │ ├── check │ │ ├── can_show_warning_for_unused_input │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ └── unused-input.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── deny-warnings │ │ │ └── warning_becomes_error_with_flag │ │ │ │ ├── args │ │ │ │ ├── exit_code │ │ │ │ ├── inputs │ │ │ │ └── unused-input.wdl │ │ │ │ ├── stderr │ │ │ │ └── stdout │ │ └── except │ │ │ ├── can_ignore_rule │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ └── unused-input.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ │ └── can_ignore_rule_case_insensitive │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ └── unused-input.wdl │ │ │ ├── stderr │ │ │ └── stdout │ ├── config-init │ │ ├── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ └── run │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ ├── config-resolve │ │ ├── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── multi │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ ├── first.toml │ │ │ │ ├── second.toml │ │ │ │ └── third.toml │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── run │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ └── sprocket.toml │ │ │ ├── stderr │ │ │ └── stdout │ │ └── unredacted │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ └── sprocket.toml │ │ │ ├── stderr │ │ │ └── stdout │ ├── config │ │ └── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ ├── doc │ │ ├── custom_logo │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ ├── file.wdl │ │ │ │ └── test-logo.svg │ │ │ ├── outputs │ │ │ │ ├── docs │ │ │ │ │ ├── assets │ │ │ │ │ │ ├── category-selected.light.svg │ │ │ │ │ │ ├── category-selected.svg │ │ │ │ │ │ ├── category-unselected.light.svg │ │ │ │ │ │ ├── category-unselected.svg │ │ │ │ │ │ ├── chevron-down.light.svg │ │ │ │ │ │ ├── chevron-down.svg │ │ │ │ │ │ ├── chevron-up.light.svg │ │ │ │ │ │ ├── chevron-up.svg │ │ │ │ │ │ ├── dir-open.light.svg │ │ │ │ │ │ ├── dir-open.svg │ │ │ │ │ │ ├── folder-selected.light.svg │ │ │ │ │ │ ├── folder-selected.svg │ │ │ │ │ │ ├── folder-unselected.light.svg │ │ │ │ │ │ ├── folder-unselected.svg │ │ │ │ │ │ ├── information-circle.light.svg │ │ │ │ │ │ ├── information-circle.svg │ │ │ │ │ │ ├── link.light.svg │ │ │ │ │ │ ├── link.svg │ │ │ │ │ │ ├── list-bullet-selected.light.svg │ │ │ │ │ │ ├── list-bullet-selected.svg │ │ │ │ │ │ ├── list-bullet-unselected.light.svg │ │ │ │ │ │ ├── list-bullet-unselected.svg │ │ │ │ │ │ ├── logo.light.svg │ │ │ │ │ │ ├── logo.svg │ │ │ │ │ │ ├── missing-home.light.svg │ │ │ │ │ │ ├── missing-home.svg │ │ │ │ │ │ ├── search.light.svg │ │ │ │ │ │ ├── search.svg │ │ │ │ │ │ ├── sidebar-icon-default.light.svg │ │ │ │ │ │ ├── sidebar-icon-default.svg │ │ │ │ │ │ ├── sidebar-icon-expand.light.svg │ │ │ │ │ │ ├── sidebar-icon-expand.svg │ │ │ │ │ │ ├── sidebar-icon-hide.light.svg │ │ │ │ │ │ ├── sidebar-icon-hide.svg │ │ │ │ │ │ ├── struct-selected.light.svg │ │ │ │ │ │ ├── struct-selected.svg │ │ │ │ │ │ ├── struct-unselected.light.svg │ │ │ │ │ │ ├── struct-unselected.svg │ │ │ │ │ │ ├── task-selected.light.svg │ │ │ │ │ │ ├── task-selected.svg │ │ │ │ │ │ ├── task-unselected.light.svg │ │ │ │ │ │ ├── task-unselected.svg │ │ │ │ │ │ ├── wdl-dir-selected.light.svg │ │ │ │ │ │ ├── wdl-dir-selected.svg │ │ │ │ │ │ ├── wdl-dir-unselected.light.svg │ │ │ │ │ │ ├── wdl-dir-unselected.svg │ │ │ │ │ │ ├── workflow-selected.light.svg │ │ │ │ │ │ ├── workflow-selected.svg │ │ │ │ │ │ ├── workflow-unselected.light.svg │ │ │ │ │ │ ├── workflow-unselected.svg │ │ │ │ │ │ ├── x-mark.light.svg │ │ │ │ │ │ └── x-mark.svg │ │ │ │ │ ├── file │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ └── test-workflow.html │ │ │ │ │ ├── index.html │ │ │ │ │ ├── index.js │ │ │ │ │ └── style.css │ │ │ │ ├── file.wdl │ │ │ │ └── test-logo.svg │ │ │ ├── stderr │ │ │ └── stdout │ │ └── ignorefile │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ ├── .sprocketignore │ │ │ ├── file.wdl │ │ │ └── malformed.wdl │ │ │ ├── outputs │ │ │ ├── .sprocketignore │ │ │ ├── docs │ │ │ │ ├── assets │ │ │ │ │ ├── category-selected.light.svg │ │ │ │ │ ├── category-selected.svg │ │ │ │ │ ├── category-unselected.light.svg │ │ │ │ │ ├── category-unselected.svg │ │ │ │ │ ├── chevron-down.light.svg │ │ │ │ │ ├── chevron-down.svg │ │ │ │ │ ├── chevron-up.light.svg │ │ │ │ │ ├── chevron-up.svg │ │ │ │ │ ├── dir-open.light.svg │ │ │ │ │ ├── dir-open.svg │ │ │ │ │ ├── folder-selected.light.svg │ │ │ │ │ ├── folder-selected.svg │ │ │ │ │ ├── folder-unselected.light.svg │ │ │ │ │ ├── folder-unselected.svg │ │ │ │ │ ├── information-circle.light.svg │ │ │ │ │ ├── information-circle.svg │ │ │ │ │ ├── link.light.svg │ │ │ │ │ ├── link.svg │ │ │ │ │ ├── list-bullet-selected.light.svg │ │ │ │ │ ├── list-bullet-selected.svg │ │ │ │ │ ├── list-bullet-unselected.light.svg │ │ │ │ │ ├── list-bullet-unselected.svg │ │ │ │ │ ├── logo.light.svg │ │ │ │ │ ├── logo.svg │ │ │ │ │ ├── missing-home.light.svg │ │ │ │ │ ├── missing-home.svg │ │ │ │ │ ├── search.light.svg │ │ │ │ │ ├── search.svg │ │ │ │ │ ├── sidebar-icon-default.light.svg │ │ │ │ │ ├── sidebar-icon-default.svg │ │ │ │ │ ├── sidebar-icon-expand.light.svg │ │ │ │ │ ├── sidebar-icon-expand.svg │ │ │ │ │ ├── sidebar-icon-hide.light.svg │ │ │ │ │ ├── sidebar-icon-hide.svg │ │ │ │ │ ├── struct-selected.light.svg │ │ │ │ │ ├── struct-selected.svg │ │ │ │ │ ├── struct-unselected.light.svg │ │ │ │ │ ├── struct-unselected.svg │ │ │ │ │ ├── task-selected.light.svg │ │ │ │ │ ├── task-selected.svg │ │ │ │ │ ├── task-unselected.light.svg │ │ │ │ │ ├── task-unselected.svg │ │ │ │ │ ├── wdl-dir-selected.light.svg │ │ │ │ │ ├── wdl-dir-selected.svg │ │ │ │ │ ├── wdl-dir-unselected.light.svg │ │ │ │ │ ├── wdl-dir-unselected.svg │ │ │ │ │ ├── workflow-selected.light.svg │ │ │ │ │ ├── workflow-selected.svg │ │ │ │ │ ├── workflow-unselected.light.svg │ │ │ │ │ ├── workflow-unselected.svg │ │ │ │ │ ├── x-mark.light.svg │ │ │ │ │ └── x-mark.svg │ │ │ │ ├── file │ │ │ │ │ ├── index.html │ │ │ │ │ └── test-workflow.html │ │ │ │ ├── index.html │ │ │ │ ├── index.js │ │ │ │ └── style.css │ │ │ ├── file.wdl │ │ │ └── malformed.wdl │ │ │ ├── stderr │ │ │ └── stdout │ ├── explain │ │ ├── CallInputSpacing-CaseInsensitive │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── CallInputSpacing │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── definitions │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ └── tag │ │ │ ├── Clarity │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ │ └── Completeness │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ ├── format │ │ ├── check │ │ │ └── format_check_does_not_overwrite_file.disabled │ │ │ │ ├── args │ │ │ │ ├── exit_code │ │ │ │ ├── inputs │ │ │ │ └── file.wdl │ │ │ │ ├── outputs │ │ │ │ └── file.wdl │ │ │ │ ├── stderr │ │ │ │ └── stdout │ │ └── overwrite │ │ │ └── can_format_file_in_place │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ └── file.wdl │ │ │ ├── outputs │ │ │ └── file.wdl │ │ │ ├── stderr │ │ │ └── stdout │ ├── help │ │ ├── args │ │ ├── exit_code │ │ ├── stderr │ │ └── stdout │ ├── inputs │ │ ├── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── json │ │ │ ├── complex-types │ │ │ │ ├── args │ │ │ │ ├── exit_code │ │ │ │ ├── inputs │ │ │ │ │ └── complex-types.wdl │ │ │ │ ├── stderr │ │ │ │ └── stdout │ │ │ └── nested-input │ │ │ │ ├── args │ │ │ │ ├── exit_code │ │ │ │ ├── inputs │ │ │ │ └── nested.wdl │ │ │ │ ├── stderr │ │ │ │ └── stdout │ │ └── yaml │ │ │ └── complex-types │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ └── complex-types.wdl │ │ │ ├── stderr │ │ │ └── stdout │ ├── run │ │ ├── compare-coerced │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ └── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ ├── ensure-absolute-inputs │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ ├── files │ │ │ │ │ └── first.txt │ │ │ │ ├── inputs.json │ │ │ │ ├── second.txt │ │ │ │ └── source.wdl │ │ │ ├── stderr │ │ │ └── stdout │ │ └── help │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── stderr │ │ │ └── stdout │ ├── test │ │ ├── bad_test_definitions │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ │ ├── bar.wdl │ │ │ │ ├── bar.yaml │ │ │ │ ├── foo.wdl │ │ │ │ └── foo.yaml │ │ │ ├── stderr │ │ │ └── stdout │ │ └── matrix_combinations │ │ │ ├── args │ │ │ ├── exit_code │ │ │ ├── inputs │ │ │ ├── example.wdl │ │ │ ├── example.yaml │ │ │ ├── flag_filter.wdl │ │ │ └── test │ │ │ │ └── flag_filter.yml │ │ │ ├── stderr │ │ │ └── stdout │ └── validate │ │ ├── compare-coerced │ │ ├── args │ │ ├── exit_code │ │ ├── inputs │ 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-------------------------------------------------------------------------------- 1 | { 2 | "test.runtime.returnCodes": null 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/invalid-runtime-type/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.runtime.returnCodes: null -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/invalid-wdl-array/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.x": [1, "2", false] 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/known-requirement/error.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/known-requirement/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.requirements.container": "foo/bar" 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/known-requirement/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.requirements.container: "foo/bar" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-call-input/error.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-call-input/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | } 3 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-call-input/inputs.yaml: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-file/inputs.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-prefix/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.x: 1 2 | y: 2 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/missing-task-input/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.x": "foo" 3 | } 4 | 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testB.y: 2 3 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/nested-input-already-specified/inputs.yaml: -------------------------------------------------------------------------------- 1 | bar.foo.x: "bad" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/nested-inputs-not-allowed/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.foo.bar": 1 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/nested-inputs-not-allowed/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.foo.bar: 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-call-1_2/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.foo.bar": 1 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-call-1_2/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.foo.bar: 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-call/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.foo.bar": 1 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-call/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.foo.bar: 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-hint/error.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-hint/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.hints.foo": "bar" 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-hint/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.hints.foo: "bar" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-nested-input/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "bar.foo.baz": 1 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-nested-input/inputs.yaml: -------------------------------------------------------------------------------- 1 | bar.foo.baz: 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-requirement/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.requirements.foo": "bar" 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-requirement/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.requirements.foo: "bar" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-task-input/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.x": 5 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-task-input/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.x: 5 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-task-or-workflow/inputs.yaml: -------------------------------------------------------------------------------- 1 | baz.foo: "bar" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-workflow-input/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.x": 5 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/inputs/unknown-workflow-input/inputs.yaml: -------------------------------------------------------------------------------- 1 | test.x: 5 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stjude-rust-labs/sprocket/HEAD/crates/wdl-engine/tests/tasks.rs -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-access/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-access/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "array_access.s": "hello" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-access/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-access/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-map-equality/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-map-equality/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-map-equality/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/array-map-equality/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/change-extension-task/files/foo.data: -------------------------------------------------------------------------------- 1 | data -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/change-extension-task/files/foo.index: -------------------------------------------------------------------------------- 1 | index -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/change-extension-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "change_extension.prefix": "foo" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/change-extension-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/change-extension-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/clobber/files/foo.txt: -------------------------------------------------------------------------------- 1 | bar 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/clobber/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/clobber/outputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/clobber/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/clobber/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-coerced/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-coerced/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-coerced/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-coerced/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-optionals/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-optionals/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-optionals/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/compare-optionals/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/concat-optional/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/concat-optional/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/concat-optional/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/concat-optional/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/cpu_limit/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/cpu_limit/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/declarations/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/declarations/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "declarations.pi": 3.14 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/declarations/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/declarations/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/files/result1: -------------------------------------------------------------------------------- 1 | foobar -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/files/result2: -------------------------------------------------------------------------------- 1 | foobar -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/files/result3: -------------------------------------------------------------------------------- 1 | foobar -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/default-option-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/command: -------------------------------------------------------------------------------- 1 | cat $f -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/foo.txt: -------------------------------------------------------------------------------- 1 | hello world 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.f": "foo.txt" 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.out": "hello world" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/env_var_guest_path/stdout: -------------------------------------------------------------------------------- 1 | hello world 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/expressions-task/files/hello.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/expressions-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "expressions.x": 5 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/expressions-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/expressions-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-output-task/files/foo.goodbye: -------------------------------------------------------------------------------- 1 | goodbye -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-output-task/files/foo.hello: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-output-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-output-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes-task/files/created_file: -------------------------------------------------------------------------------- 1 | this file is 22 bytes 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes-task/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes/files/created_file: -------------------------------------------------------------------------------- 1 | this file is 22 bytes 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/file-sizes/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/flags-task/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "flags.num_matches": 2 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/flags-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/flags-task/stdout: -------------------------------------------------------------------------------- 1 | 2 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/funky-input-filename/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings (final) (2).txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/funky-input-filename/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/files/file_1.txt: -------------------------------------------------------------------------------- 1 | 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/files/file_2.txt: -------------------------------------------------------------------------------- 1 | 2 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/files/file_3.txt: -------------------------------------------------------------------------------- 1 | 3 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "glob.num_files": 3 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/glob-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/hello/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/hello/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/if-type-mismatch/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/import-structs/hello.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/import-structs/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/import-structs/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/a.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/b.txt: -------------------------------------------------------------------------------- 1 | world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/c.txt: -------------------------------------------------------------------------------- 1 | ! 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.out": "hello world!" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-path-mapping/stdout: -------------------------------------------------------------------------------- 1 | hello world! 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-type-qualifiers/files/result: -------------------------------------------------------------------------------- 1 | A 2 | B 3 | C 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-type-qualifiers/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/input-type-qualifiers/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/invalid-placeholder-default/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/invalid-placeholder-sep/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/invalid-placeholder-true-false/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/member-access/command: -------------------------------------------------------------------------------- 1 | printf "bar" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/member-access/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/member-access/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/member-access/stdout: -------------------------------------------------------------------------------- 1 | bar -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/memory_limit/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/memory_limit/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/missing-output-file/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/missing-output-file/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-placeholders/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-placeholders/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-placeholders/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-placeholders/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings1/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings1/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings1/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings1/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings2/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings2/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings2/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings2/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings3/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings3/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings3/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings3/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings4/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings4/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings4/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/multiline-strings4/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-access/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-access/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-access/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-placeholders/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-placeholders/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_placeholders.s": "4" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-placeholders/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/nested-placeholders/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/non-empty-optional/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/non-empty-optional/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/non-empty-optional/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/non-empty-optional/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optional-output-task/files/example1.txt: -------------------------------------------------------------------------------- 1 | 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optional-output-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "optional_output.make_example2": false 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optional-output-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optional-output-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optionals/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optionals/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optionals/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/optionals/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/files/a.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/files/b.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/files/threshold.txt: -------------------------------------------------------------------------------- 1 | 5 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "outputs.t": 5 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/outputs-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/override_cpu_limit/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/override_cpu_limit/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/override_memory_limit/command: -------------------------------------------------------------------------------- 1 | grep -E 'hello.*' 'greetings.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/override_memory_limit/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/path-translation/a.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/path-translation/b.txt: -------------------------------------------------------------------------------- 1 | world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/path-translation/c.txt: -------------------------------------------------------------------------------- 1 | ! -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/path-translation/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/person-struct-task/hello.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/person-struct-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-coercion/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-coercion/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-coercion/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-coercion/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-none/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-none/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-none/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholder-none/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholders/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholders/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/placeholders/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-literals/files/testdir/hello.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-literals/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-literals/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-literals/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-to-string/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-to-string/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "primitive_to_string.i": 3 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-to-string/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/primitive-to-string/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/private-declaration-task/command: -------------------------------------------------------------------------------- 1 | head -3 'tmp0' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/private-declaration-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/private-declaration-task/stdout: -------------------------------------------------------------------------------- 1 | A 2 | B 3 | C 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/relative-and-absolute-task/files/my/path/to/something.txt: -------------------------------------------------------------------------------- 1 | something -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/relative-and-absolute-task/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/relative-and-absolute-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/relative-and-absolute-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/retry/files/done.txt: -------------------------------------------------------------------------------- 1 | attempt 3 was successful! 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/retry/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/retry/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.done": "attempts/3/work/done.txt" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/retry/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/retry/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sep-option-to-function/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sep-option-to-function/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sep-option-to-function/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/split-task/command: -------------------------------------------------------------------------------- 1 | echo "hello there world" > file.txt -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/split-task/files/file.txt: -------------------------------------------------------------------------------- 1 | hello there world 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/split-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/split-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/split-task/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/data/file: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "string_to_file.paths_equal": true 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/string-to-file/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/struct-to-struct/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/struct-to-struct/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/struct-to-struct/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/struct-to-struct/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sum-task/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "sum.total": 6 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sum-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/sum-task/stdout: -------------------------------------------------------------------------------- 1 | 6 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-fail/command: -------------------------------------------------------------------------------- 1 | >&2 echo this task is going to fail! 2 | exit 1 -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-fail/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-fail/stderr: -------------------------------------------------------------------------------- 1 | this task is going to fail! 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-fail/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-inputs-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "task_inputs.i": 1 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-inputs-task/outputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-inputs-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-inputs-task/stdout: -------------------------------------------------------------------------------- 1 | hello 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-retry-with-memory-increase/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-retry-with-memory-increase/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-command/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-command/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-output/command: -------------------------------------------------------------------------------- 1 | echo "test" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-output/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-output/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-output/stdout: -------------------------------------------------------------------------------- 1 | test 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-requirements/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-scope-requirements/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-variable/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-variable/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-with-comments/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "task_with_comments.number": 1 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-with-comments/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "task_with_comments.result": 2 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-with-comments/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/task-with-comments/stdout: -------------------------------------------------------------------------------- 1 | 2 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/ternary/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/ternary/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "ternary.morning": true 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/ternary/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/ternary/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-basename/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-basename/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-basename/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-basename/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-ceil/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-ceil/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_ceil.i1": 2 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-ceil/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-ceil/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-find/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-find/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-find/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-find/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-floor/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-floor/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_floor.i1": 2 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-floor/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-floor/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-join-paths/command: -------------------------------------------------------------------------------- 1 | cat 'mydata.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-join-paths/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-join-paths/mydata.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-join-paths/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-join-paths/stdout: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-map/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-map/data/file1: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-map/data/file2: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-map/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-map/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- 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/crates/wdl-engine/tests/tasks/test-object/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-object/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-pairs/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-pairs/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-pairs/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-pairs/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-placeholders-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_placeholders.infile": "greetings.txt" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-placeholders-task/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-round/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-round/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_round.i1": 2 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-round/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-round/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stderr/command: -------------------------------------------------------------------------------- 1 | >&2 printf "hello world" -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stderr/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stderr/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_stderr.message": "hello world" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stderr/stderr: -------------------------------------------------------------------------------- 1 | hello world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stderr/stdout: -------------------------------------------------------------------------------- 1 | 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-------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-stdout/stdout: -------------------------------------------------------------------------------- 1 | hello world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-struct/command: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-struct/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/test-struct/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/true-false-ternary/files/result1: -------------------------------------------------------------------------------- 1 | hello world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/true-false-ternary/files/result2: -------------------------------------------------------------------------------- 1 | hello world -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/true-false-ternary/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/true-false-ternary/stdout: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/command: -------------------------------------------------------------------------------- 1 | cat 'message.txt' -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.file": "../unclean-input-path/message.txt" 3 | } 4 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/message.txt: -------------------------------------------------------------------------------- 1 | Hello world! -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.message": "Hello world!" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/unclean-input-path/stdout: -------------------------------------------------------------------------------- 1 | Hello world! -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/work-dir-perms/command: -------------------------------------------------------------------------------- 1 | touch foo -------------------------------------------------------------------------------- /crates/wdl-engine/tests/tasks/work-dir-perms/files/foo: 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-------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/array-literal-coersion/outputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/array-map-equality/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/as-map/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/call-imported-task/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_imported_task.x": 5 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/call-imported-task/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_imported_task.result": 20 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/callstack/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/compare-coerced/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/declarations/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "declarations.pi": 3.14 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/empty-array-fail/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/env-vars/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_variable_should_echo.greeting": "hello world" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/env-vars/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_variable_should_echo.out": "hello world" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/example-ternary/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "ternary.morning": true 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/if-else/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/if-else/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "if_else.greeting": "Good afternoon buddy!" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/if-expr-array/inputs.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/if-expr-array/outputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/illegal-access/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "illegal_access.my": {} 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/import-structs/hello.txt: -------------------------------------------------------------------------------- 1 | hello -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/import-structs/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/import-structs/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "import_structs.bill": 175000.0 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/input-ref-call/inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "input_ref_call.x": 5 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/input-ref-call/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "input_ref_call.result": 20 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/inputs-with-none/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/localization/foo.txt: -------------------------------------------------------------------------------- 1 | This is a local input file. 2 | -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/map-literal-coercion/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/map-literal-coercion/outputs.json: -------------------------------------------------------------------------------- 1 | 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"non_empty_optional_fail.x": [] 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/non-empty-optional/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/optional-with-defaults/outputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "optional_with_default.greeting": "John" 3 | } -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/optionals/inputs.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /crates/wdl-engine/tests/workflows/pair-to-array/inputs.json: 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/tests/cli/run/ensure-absolute-inputs/inputs/second.txt: -------------------------------------------------------------------------------- 1 | Sprocket is neato! -------------------------------------------------------------------------------- /tests/cli/run/ensure-absolute-inputs/stderr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/cli/run/help/args: -------------------------------------------------------------------------------- 1 | run --help -------------------------------------------------------------------------------- /tests/cli/run/help/exit_code: -------------------------------------------------------------------------------- 1 | 0 -------------------------------------------------------------------------------- /tests/cli/run/help/stderr: -------------------------------------------------------------------------------- 1 | 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new_two.key: "bazbarfoo" -------------------------------------------------------------------------------- /tests/fixtures/inputs_two.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/stjude-rust-labs/sprocket/HEAD/tests/fixtures/inputs_two.json -------------------------------------------------------------------------------- /tests/fixtures/missing_ext: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/fixtures/nonmap_inputs.json: -------------------------------------------------------------------------------- 1 | 42.0 -------------------------------------------------------------------------------- /tests/fixtures/nonmap_inputs.yml: -------------------------------------------------------------------------------- 1 | 42.0 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