├── .github ├── copilot-instructions.md └── workflows │ ├── actions │ └── install-sbt │ │ └── action.yml │ ├── main.yml │ ├── release.yml │ └── snapshot.yml ├── .gitignore ├── .scalafmt.conf ├── LICENSE ├── Makefile ├── README.md ├── RELEASE_NOTES.md ├── doc ├── AutoCoercionsConsideredHarmful.md ├── Commands │ ├── Check.md │ ├── Docgen.md │ ├── Exec.md │ ├── Fix.md │ ├── Format.md │ ├── Lint.md │ ├── New.md │ ├── PrintTree.md │ ├── Readmes.md │ └── Upgrade.md ├── Developing.md ├── Examples │ └── GenerateCode.scala ├── Style.md └── logo.png ├── project ├── Merging.scala ├── build.properties └── plugins.sbt └── src ├── main ├── antlr4 │ ├── draft_2 │ │ ├── WdlDraft2Lexer.g4 │ │ └── WdlDraft2Parser.g4 │ ├── v1 │ │ ├── WdlV1Lexer.g4 │ │ └── WdlV1Parser.g4 │ ├── v1_1 │ │ ├── WdlV1_1Lexer.g4 │ │ └── WdlV1_1Parser.g4 │ └── v2 │ │ ├── WdlV2Lexer.g4 │ │ └── WdlV2Parser.g4 ├── resources │ ├── application.conf │ ├── rules │ │ └── lint_rules.json │ └── templates │ │ ├── documentation │ │ ├── document.beard │ │ ├── document.ssp │ │ ├── index.ssp │ │ └── structs.ssp │ │ ├── exec │ │ ├── commandScript.ssp │ │ ├── dockerRunScript.ssp │ │ └── emptyCommandScript.ssp │ │ ├── project │ │ ├── Dockerfile.ssp │ │ └── Makefile.ssp │ │ └── readme │ │ ├── TaskReadme.developer.md.ssp │ │ ├── TaskReadme.md.ssp │ │ ├── WorkflowReadme.developer.md.ssp │ │ └── WorkflowReadme.md.ssp └── scala │ └── wdlTools │ ├── cli │ ├── CliTypeErrorHandler.scala │ ├── Docgen.scala │ ├── Exec.scala │ ├── Fix.scala │ ├── Format.scala │ ├── Generate.scala │ ├── Lint.scala │ ├── Main.scala │ ├── PrintTree.scala │ ├── Readmes.scala │ ├── TypeCheck.scala │ ├── Upgrade.scala │ └── WdlToolsConf.scala │ ├── eval │ ├── Coercion.scala │ ├── Eval.scala │ ├── EvalUtils.scala │ ├── IoSupport.scala │ ├── Meta.scala │ ├── Runtime.scala │ ├── RuntimeAttributes.scala │ ├── Stdlib.scala │ ├── WdlValueSerde.scala │ ├── WdlValues.scala │ └── package.scala │ ├── exec │ ├── InputOutput.scala │ ├── TaskContext.scala │ ├── TaskExecutor.scala │ └── package.scala │ ├── generators │ ├── Renderer.scala │ ├── code │ │ ├── Fixer.scala │ │ ├── Upgrader.scala │ │ ├── WdlFormatter.scala │ │ ├── WdlGenerator.scala │ │ └── package.scala │ └── project │ │ ├── DocumentationGenerator.scala │ │ ├── ProjectGenerator.scala │ │ ├── ReadmeGenerator.scala │ │ └── TestsGenerator.scala │ ├── linter │ ├── Linter.scala │ ├── LinterASTWalker.scala │ ├── Rules.scala │ └── package.scala │ ├── package.scala │ ├── syntax │ ├── ASTWalker.scala │ ├── AbstractSyntax.scala │ ├── AllParseTreeListener.scala │ ├── Antlr4Util.scala │ ├── Builtins.scala │ ├── Parsers.scala │ ├── SyntaxUtils.scala │ ├── WdlParser.scala │ ├── draft_2 │ │ ├── ConcreteSyntax.scala │ │ ├── ParseAll.scala │ │ ├── ParseTop.scala │ │ └── WdlDraft2Grammar.scala │ ├── package.scala │ ├── v1 │ │ ├── ConcreteSyntax.scala │ │ ├── ParseAll.scala │ │ ├── ParseTop.scala │ │ └── WdlV1Grammar.scala │ ├── v1_1 │ │ ├── ConcreteSyntax.scala │ │ ├── ParseAll.scala │ │ ├── ParseTop.scala │ │ └── WdlV1_1Grammar.scala │ └── v2 │ │ ├── ConcreteSyntax.scala │ │ ├── ParseAll.scala │ │ ├── ParseTop.scala │ │ └── WdlV2Grammar.scala │ └── types │ ├── Graph.scala │ ├── Stdlib.scala │ ├── TypeContext.scala │ ├── TypeInfer.scala │ ├── TypeUtils.scala │ ├── TypedAbstractSyntax.scala │ ├── TypedAbstractSyntaxTreeWalker.scala │ ├── Unification.scala │ ├── WdlTypeSerde.scala │ ├── WdlTypes.scala │ └── package.scala └── test ├── resources ├── ast │ └── simple.wdl.ast ├── clone-corpora.sh ├── corpora_repos.json ├── docgen │ └── v1 │ │ └── wdl │ │ ├── foo.wdl │ │ └── simple.wdl ├── eval │ ├── v1.1 │ │ ├── apps_1177_native_default_instance.wdl │ │ ├── apps_1177_native_memory_override.wdl │ │ ├── apps_1341.wdl │ │ ├── apps_579_boolean_flag_expr.wdl │ │ ├── apps_579_string_substitution_expr.wdl │ │ ├── escape_sequences.wdl │ │ ├── functions.wdl │ │ ├── no_container.wdl │ │ └── read_lines.wdl │ ├── v1 │ │ ├── add_int_and_string.wdl │ │ ├── apps_1318_nested.wdl │ │ ├── apps_1318_simple.wdl │ │ ├── bad_coercion.wdl │ │ ├── bad_protocol.wdl │ │ ├── bool_placeholder.wdl │ │ ├── bwa_mem.wdl │ │ ├── coercions.wdl │ │ ├── command2.wdl │ │ ├── command3.wdl │ │ ├── command_simple.wdl │ │ ├── conditionals3.wdl │ │ ├── constants.wdl │ │ ├── dangling.wdl │ │ ├── default_placeholder.wdl │ │ ├── empty_lines.wdl │ │ ├── empty_stdout.wdl │ │ ├── indented_command.wdl │ │ ├── leading_spaces.wdl │ │ ├── leading_spaces2.wdl │ │ ├── nested_placeholders.wdl │ │ ├── non_standard_coercions.wdl │ │ ├── operator_precedence.wdl │ │ ├── pair.wdl │ │ ├── python_heredoc.wdl │ │ ├── sep_placeholder.wdl │ │ ├── simple_expr.wdl │ │ ├── stdlib.wdl │ │ └── write_lines.wdl │ └── v2 │ │ ├── add_int_and_string.wdl │ │ ├── apps_1353_v_dir_coercion.wdl │ │ └── bug_230.wdl ├── exec │ ├── inputs_with_defaults.wdl │ ├── simple.wdl │ ├── structs.wdl │ ├── task_input_struct_optional_element.wdl │ ├── workflow_input_struct_optional_element.wdl │ └── workflow_scatter_input_struct_optional_element.wdl ├── format │ ├── after │ │ ├── add.wdl │ │ ├── call_with_function.wdl │ │ ├── fix.wdl │ │ ├── meta_object_values.wdl │ │ ├── nested_quotes.wdl │ │ ├── nonstandard.wdl │ │ ├── simple.wdl │ │ ├── single_line_command.wdl │ │ └── struct_literal.wdl │ └── before │ │ ├── add.wdl │ │ ├── bug-382.wdl │ │ ├── call_with_function.wdl │ │ ├── deep_nesting.wdl │ │ ├── empty_call.wdl │ │ ├── escape_sequences.wdl │ │ ├── fix.wdl │ │ ├── library_syscall.wdl │ │ ├── meta_object_values.wdl │ │ ├── nested_quotes.wdl │ │ ├── none_literal.wdl │ │ ├── nonstandard.wdl │ │ ├── optionals.wdl │ │ ├── python_heredoc.wdl │ │ ├── simple.wdl │ │ ├── single_line_command.wdl │ │ ├── single_string_multiline_command.wdl │ │ ├── string_add.wdl │ │ ├── struct_field.wdl │ │ ├── struct_literal.wdl │ │ ├── sum_array.wdl │ │ └── wf_with_call.wdl ├── linter │ └── v1 │ │ └── simple.wdl ├── syntax │ ├── draft_2 │ │ ├── tasks │ │ │ ├── bug16-chained-operations.wdl │ │ │ ├── expressions.wdl │ │ │ ├── get_name_bug.wdl │ │ │ ├── interpolation.wdl │ │ │ ├── multiple_sections.wdl │ │ │ ├── output_section.wdl │ │ │ ├── types.wdl │ │ │ ├── wc.wdl │ │ │ └── wrong_comment_style.wdl │ │ └── workflows │ │ │ ├── I.wdl │ │ │ ├── bad_declaration.wdl │ │ │ ├── bad_type.wdl │ │ │ ├── chained_expr.wdl │ │ │ ├── compound_expr_bug.wdl │ │ │ └── imports.wdl │ ├── v1 │ │ ├── structs │ │ │ └── I.wdl │ │ ├── tasks │ │ │ ├── bug16-chained-operations.wdl │ │ │ ├── call_native_app.wdl │ │ │ ├── comments.wdl │ │ │ ├── dx_app_extern.wdl │ │ │ ├── expressions.wdl │ │ │ ├── get_name_bug.wdl │ │ │ ├── interpolation.wdl │ │ │ ├── meta_null_value.wdl │ │ │ ├── meta_section_compound.wdl │ │ │ ├── meta_section_error.wdl │ │ │ ├── metadata_complex.wdl │ │ │ ├── metadata_complex_2.wdl │ │ │ ├── metadata_null_value.wdl │ │ │ ├── missing_type_bug.wdl │ │ │ ├── multiple_sections.wdl │ │ │ ├── nested_placeholders.wdl │ │ │ ├── output_section.wdl │ │ │ ├── runtime_section_duplicate_key.wdl │ │ │ ├── spaces.wdl │ │ │ ├── suggestions_meta.wdl │ │ │ ├── types.wdl │ │ │ ├── wc.wdl │ │ │ └── wrong_comment_style.wdl │ │ └── workflows │ │ │ ├── I.wdl │ │ │ ├── bad_declaration.wdl │ │ │ ├── bad_type.wdl │ │ │ ├── call_bug.wdl │ │ │ ├── call_bug2.wdl │ │ │ ├── chained_expr.wdl │ │ │ ├── compound_expr_bug.wdl │ │ │ ├── empty_call_input.wdl │ │ │ ├── escape_sequences.wdl │ │ │ ├── escape_sequences2.wdl │ │ │ ├── extra_comma.wdl │ │ │ ├── imports.wdl │ │ │ ├── meta_key_conflicts.wdl │ │ │ ├── relative_imports.wdl │ │ │ ├── relative_imports_II.wdl │ │ │ ├── tools │ │ │ ├── count_dogs.wdl │ │ │ └── library.wdl │ │ │ ├── two_level.wdl │ │ │ └── unterminated_dquote.wdl │ ├── v1_1 │ │ ├── custom_runtime.wdl │ │ ├── nested_expr.wdl │ │ └── sep.wdl │ └── v2 │ │ ├── complex_hint_values.wdl │ │ ├── library.wdl │ │ ├── movies.wdl │ │ ├── parameter_meta_comment.wdl │ │ ├── passthrough.wdl │ │ └── types.wdl ├── types │ ├── draft2 │ │ ├── array_add.wdl │ │ ├── array_mul.wdl │ │ ├── call_with_defaults.wdl │ │ ├── conditional.wdl │ │ ├── library_math.wdl │ │ ├── modulo.wdl │ │ ├── object_fields.wdl │ │ └── population.wdl │ ├── graph │ │ ├── many_structs.wdl │ │ ├── nested.wdl │ │ ├── nested_no_fw_ref.wdl │ │ └── tasks.wdl │ ├── v1 │ │ ├── array_coersion.wdl │ │ ├── bad_stdlib_calls.wdl │ │ ├── census.wdl │ │ ├── coercions_questionable.wdl │ │ ├── coercions_strict.wdl │ │ ├── command_string.wdl │ │ ├── comparison1.wdl │ │ ├── comparison2.wdl │ │ ├── comparison4.wdl │ │ ├── comparisons.wdl │ │ ├── compound_expr_bug.wdl │ │ ├── declaration_shadowing.wdl │ │ ├── echo-pairs.wdl │ │ ├── empty_array_coercion.wdl │ │ ├── empty_array_in_call.wdl │ │ ├── expressions.wdl │ │ ├── expressions_bad.wdl │ │ ├── import_folder.wdl │ │ ├── imports.wdl │ │ ├── imports │ │ │ └── library2.wdl │ │ ├── input_section.wdl │ │ ├── invalid_param_meta.wdl │ │ ├── library.wdl │ │ ├── linear.wdl │ │ ├── map_index.wdl │ │ ├── meta_null_value.wdl │ │ ├── meta_section_compound.wdl │ │ ├── missing_args.wdl │ │ ├── nested.wdl │ │ ├── nested_compound_string.wdl │ │ ├── nested_optional.wdl │ │ ├── nonempty_array_coercion.wdl │ │ ├── optional_placeholder_value.wdl │ │ ├── output_section.wdl │ │ ├── polymorphic_types.wdl │ │ ├── runtime_section_I.wdl │ │ ├── runtime_section_bad.wdl │ │ ├── scatter_I.wdl │ │ ├── scatter_II.wdl │ │ ├── shadow.wdl │ │ ├── shadow_II.wdl │ │ ├── simple.wdl │ │ ├── stdlib.wdl │ │ ├── structs │ │ │ ├── file1.wdl │ │ │ ├── file2.wdl │ │ │ └── file3.wdl │ │ ├── subworkflows │ │ │ ├── sub.wdl │ │ │ └── tasks.wdl │ │ ├── top_level.wdl │ │ └── udfs.wdl │ └── v2 │ │ ├── add_int_and_string.wdl │ │ ├── apps_1421_dir_output.wdl │ │ ├── concat_optional_types_in_command.wdl │ │ ├── output_section.wdl │ │ ├── runtime_interpolation.wdl │ │ ├── structs │ │ ├── inputs.json │ │ ├── keyword_in_struct.wdl │ │ ├── parent_workflow.wdl │ │ ├── struct_literal.wdl │ │ ├── test1 │ │ │ ├── inputs1.json │ │ │ ├── test_struct1.wdl │ │ │ └── test_workflow1.wdl │ │ └── test2 │ │ │ ├── inputs2.json │ │ │ ├── test_struct2.wdl │ │ │ └── test_workflow2.wdl │ │ └── v2comparison.wdl └── upgrade │ ├── after │ ├── command4.wdl │ └── simple.wdl │ └── before │ ├── command4.wdl │ └── simple.wdl └── scala └── wdlTools ├── eval ├── EvalTest.scala ├── IoSupportTest.scala └── RuntimeTest.scala ├── exec └── ExecTest.scala ├── format ├── FixerTest.scala ├── FormatterTest.scala └── GeneratorTest.scala ├── linter └── v1 │ └── BaseTest.scala ├── package.scala ├── syntax ├── AbstractSyntaxTest.scala ├── draft_2 │ └── ConcreteSyntaxDraft2Test.scala ├── v1 │ └── ConcreteSyntaxV1Test.scala ├── v1_1 │ └── ConcreteSyntaxV1_1Test.scala └── v2 │ └── ConcreteSyntaxV2Test.scala ├── types ├── CorporaTest.scala ├── GatkTest.scala ├── GraphTest.scala ├── TypeInferComplianceTest.scala ├── TypeInferTest.scala ├── TypeUtilsTest.scala └── WdlTypesTest.scala └── upgrade └── BaseTest.scala /.github/copilot-instructions.md: 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