├── .github └── workflows │ ├── codeql.yml │ ├── cwl_conformance.yml │ ├── dxcint.yml │ ├── integration2.yml │ ├── linters.yml │ ├── release.yml │ └── scala.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .scalafmt.conf ├── LICENSE ├── README.md ├── RELEASE_NOTES.md ├── build.sbt ├── compiler └── src │ ├── main │ ├── resources │ │ ├── application.conf │ │ ├── logback.xml │ │ └── templates │ │ │ ├── applet_script.ssp │ │ │ ├── dynamic_applet_script.ssp │ │ │ ├── ecr_docker_preamble.ssp │ │ │ ├── generic_docker_preamble.ssp │ │ │ ├── manifest_dxda_script.ssp │ │ │ ├── static_applet_script.ssp │ │ │ ├── workflow_command_script.ssp │ │ │ └── workflow_fragment_script.ssp │ └── scala │ │ ├── dx │ │ ├── compiler │ │ │ ├── ApplicationCompiler.scala │ │ │ ├── Compiler.scala │ │ │ ├── DxExecutableDirectory.scala │ │ │ ├── ExecutableCompiler.scala │ │ │ ├── ExecutableTree.scala │ │ │ └── WorkflowCompiler.scala │ │ ├── dxni │ │ │ ├── DxNativeInterface.scala │ │ │ └── wdl │ │ │ │ └── WdlNativeInterfaceGenerator.scala │ │ └── translator │ │ │ ├── CallableAttributes.scala │ │ │ ├── Extras.scala │ │ │ ├── InputTranslator.scala │ │ │ ├── ParameterAttributes.scala │ │ │ ├── Translator.scala │ │ │ ├── WorkflowTranslator.scala │ │ │ ├── cwl │ │ │ ├── CwlTranslator.scala │ │ │ └── ProcessTranslator.scala │ │ │ └── wdl │ │ │ ├── CallableTranslator.scala │ │ │ ├── MetaTranslator.scala │ │ │ ├── RuntimeTranslator.scala │ │ │ └── WdlTranslator.scala │ │ └── dxCompiler │ │ └── Main.scala │ └── test │ ├── resources │ ├── bugs │ │ ├── apps-1191_scatter_optional_input.json │ │ ├── apps-370.wdl │ │ ├── apps-378.wdl │ │ ├── apps-573.wdl │ │ ├── apps-573_results.json │ │ ├── apps-788.wdl │ │ ├── apps_1128_wrap_native_exec.wdl │ │ ├── apps_1177_native_frag_indirect_override_unit.wdl │ │ ├── apps_1177_native_indirect_override_unit.wdl │ │ ├── apps_1197_native_frag_default_unit.wdl │ │ ├── apps_1222_optional_default_none_inner.wdl │ │ ├── apps_1222_optional_default_none_outer.wdl │ │ ├── apps_1351.wdl │ │ ├── apps_994_v1.wdl │ │ ├── apps_994_v2.wdl │ │ ├── dx_runtime_keys.wdl │ │ ├── missing_chars_in_task.wdl │ │ ├── native_with_file_output.wdl │ │ ├── scatter_inside_if.wdl │ │ ├── scatter_variable_not_found.wdl │ │ ├── subwf.wdl │ │ └── unpassed_argument_propagation.wdl │ ├── clone-corpora.sh │ ├── compiler │ │ ├── BroadGenomicsDocker.wdl │ │ ├── GPU.wdl │ │ ├── GPU2.wdl │ │ ├── Readme.wf_readme.add.md │ │ ├── Readme.wf_readme.wf_readme.md │ │ ├── add.wdl │ │ ├── add_app_meta.wdl │ │ ├── add_changed.wdl │ │ ├── add_default.wdl │ │ ├── add_dx_type.wdl │ │ ├── add_group.wdl │ │ ├── add_help.wdl │ │ ├── add_label.wdl │ │ ├── add_runtime_hints.wdl │ │ ├── add_timeout.wdl │ │ ├── add_timeout_override.wdl │ │ ├── apps_1858_inner.wdl │ │ ├── apps_1858_tat_wf.wdl │ │ ├── apps_1858_tat_wf_frags.wdl │ │ ├── apps_2477_headJobOnDemand.wdl │ │ ├── call_level2.wdl │ │ ├── cast.wdl │ │ ├── check_imports.wdl │ │ ├── choice_obj_values.wdl │ │ ├── choice_values.wdl │ │ ├── choices_type_mismatch.wdl │ │ ├── default_type_mismatch.wdl │ │ ├── dict.wdl │ │ ├── dict2.wdl │ │ ├── dx_type_nonfile.wdl │ │ ├── environment_passing_deep_nesting.wdl │ │ ├── expr_output_block.wdl │ │ ├── extras │ │ │ ├── apps_1858_for_frags.json │ │ │ ├── apps_1858_per_wf_attrs.json │ │ │ ├── apps_1858_top_wf_attrs.json │ │ │ ├── apps_2477_default_task_on_demand.json │ │ │ ├── apps_2477_per_task_on_demand.json │ │ │ ├── extras_custom_reorg.json │ │ │ ├── extras_custom_reorg_config.json │ │ │ ├── extras_license.json │ │ │ ├── short_timeout.json │ │ │ └── task_specific_short_timeout.json │ │ ├── help_input_params.wdl │ │ ├── help_output_params.wdl │ │ ├── imports │ │ │ ├── A.wdl │ │ │ ├── A_inputs.json │ │ │ ├── lib.wdl │ │ │ ├── lib │ │ │ │ └── library.wdl │ │ │ └── subworkflow.wdl │ │ ├── instance_type_test.wdl │ │ ├── library.wdl │ │ ├── meta_section.wdl │ │ ├── multi_import.wdl │ │ ├── nested_scatter.wdl │ │ ├── optional_call_output.wdl │ │ ├── optional_output.wdl │ │ ├── optionals.wdl │ │ ├── pattern_obj_params.wdl │ │ ├── pattern_params.wdl │ │ ├── reserved.wdl │ │ ├── scatter_no_call.wdl │ │ ├── scatter_subworkflow_with_optional.wdl │ │ ├── streaming_files.wdl │ │ ├── streaming_files_error1.wdl │ │ ├── streaming_files_error2.wdl │ │ ├── streaming_files_obj.wdl │ │ ├── strings.wdl │ │ ├── subblock_several_calls.wdl │ │ ├── suggestion_obj_values.wdl │ │ ├── suggestion_values.wdl │ │ ├── suggestions_missing_arg.wdl │ │ ├── suggestions_type_mismatch.wdl │ │ ├── wf_constants.wdl │ │ ├── wf_custom_reorg.wdl │ │ ├── wf_linear.wdl │ │ ├── wf_linear_no_expr.wdl │ │ ├── wf_meta.wdl │ │ ├── wf_param_meta.wdl │ │ ├── wf_readme.wdl │ │ ├── wf_to_flatten.wdl │ │ └── wf_with_output_expressions.wdl │ ├── corpora_repos.json │ ├── cwl │ │ ├── any-type-compat.cwl.json │ │ ├── basename-fields-test.cwl.json │ │ ├── cat.cwl.json │ │ ├── cond-wf-003_nojs.cwl.json │ │ ├── cond-wf-011_nojs.cwl.json │ │ ├── count-lines1-wf-dup.cwl.json │ │ ├── count-lines1-wf.cwl.json │ │ ├── count-lines11-null-step-wf-noET.cwl.json │ │ ├── count-lines17-wf.cwl.json │ │ ├── count-lines19-wf.cwl.json │ │ ├── count-lines8-wf-dup.cwl.json │ │ ├── count-lines8-wf.cwl.json │ │ ├── count-lines9-wf-noET.cwl.json │ │ ├── dynresreq-workflow-stepdefault.cwl.json │ │ ├── enum-stepdefault.cwl.json │ │ ├── io-file-default-wf.cwl.json │ │ ├── io-union-input-default-wf.cwl.json │ │ ├── js-expr-req-wf.cwl.json │ │ ├── params.cwl.json │ │ ├── params2.cwl.json │ │ ├── pass-unconnected.cwl.json │ │ ├── record-in-format.cwl.json │ │ ├── scatter-valuefrom-wf2-dup.cwl.json │ │ ├── scatter-valuefrom-wf2.cwl.json │ │ ├── scatter-wf4.cwl.json │ │ └── timelimit2-wf.cwl.json │ ├── draft2 │ │ ├── block_category.wdl │ │ ├── block_closure.wdl │ │ ├── conditionals1.wdl │ │ ├── conditionals2.wdl │ │ ├── conditionals3.wdl │ │ ├── conditionals4.wdl │ │ ├── conditionals_base.wdl │ │ ├── library.wdl │ │ ├── library_math.wdl │ │ ├── movies.wdl │ │ ├── output_only.wdl │ │ ├── output_references.wdl │ │ ├── pair.wdl │ │ ├── shapes.wdl │ │ ├── streaming.wdl │ │ └── various_calls.wdl │ ├── frag_runner │ │ ├── House.wdl │ │ ├── apps_1128_frag_default.wdl │ │ ├── conditional_no_call.wdl │ │ ├── ma.json │ │ ├── missing_args.wdl │ │ ├── nested_no_call.wdl │ │ ├── scatter_no_call.wdl │ │ ├── scatter_variable_not_found.wdl │ │ ├── scatter_with_eval.wdl │ │ ├── strings.wdl │ │ └── wf_linear.wdl │ ├── input_file │ │ ├── L2.wdl │ │ ├── L3.wdl │ │ ├── L3_inputs.json │ │ ├── add.wdl │ │ ├── add_inputs.json │ │ ├── any-type-compat_input.json │ │ ├── bool-empty-inputbinding.cwl.json │ │ ├── bool-empty-inputbinding_input.json │ │ ├── bwa-mem-tool.cwl.json │ │ ├── bwa-mem-tool_input.json │ │ ├── cat-from-dir.cwl.json │ │ ├── cat-from-dir_input1.json │ │ ├── cat-from-dir_input2.json │ │ ├── dir.cwl.json │ │ ├── dir4.cwl.json │ │ ├── dir4_input1.json │ │ ├── dir_input.json │ │ ├── echo-tool-packed.cwl.json │ │ ├── echo-tool-packed_input.json │ │ ├── echo_pairs.wdl │ │ ├── echo_pairs_input.json │ │ ├── enum-string.cwl.json │ │ ├── enum-string_input.json │ │ ├── env-tool.cwl.json │ │ ├── env-tool_input.yaml │ │ ├── initialwork-path.cwl.json │ │ ├── initialwork-path_input.json │ │ ├── input-file-metadata.cwl.json │ │ ├── input-file-metadata_input.json │ │ ├── io-any-wf.cwl.json │ │ ├── io-any-wf_input3.json │ │ ├── map_argument.wdl │ │ ├── map_argument2.wdl │ │ ├── map_argument2_input.json │ │ ├── map_argument_input.json │ │ ├── map_input.wdl │ │ ├── math.wdl │ │ ├── math_inputs.json │ │ ├── math_inputs2.json │ │ ├── missing_args.wdl │ │ ├── missing_args_inputs.json │ │ ├── no_file_key.wdl │ │ ├── no_file_key_input.json │ │ ├── override.wdl │ │ ├── override_input.json │ │ ├── population.wdl │ │ ├── population_inputs.json │ │ ├── population_top.wdl │ │ ├── runtime_override.wdl │ │ ├── runtime_override_inputs.json │ │ ├── several_tasks.wdl │ │ └── several_tasks_inputs.json │ ├── logback-test.xml │ ├── manifest │ │ ├── apps_1269_1270_unqualified_ids_manifest_unit.wdl │ │ ├── apps_1269_1270_unqualified_ids_manifest_unit_input.json │ │ ├── simple_manifest.wdl │ │ └── simple_manifest_input.json │ ├── nested │ │ ├── apps_867_w1.wdl │ │ ├── apps_867_w2.wdl │ │ ├── extras │ │ │ ├── four_levels_extras1.json │ │ │ └── four_levels_extras2.json │ │ ├── four_levels.wdl │ │ ├── four_levels_input.json │ │ ├── nested_scatter.wdl │ │ ├── param_passing.wdl │ │ ├── three_levels.wdl │ │ ├── three_levels_input.json │ │ └── two_levels.wdl │ ├── non_spec │ │ ├── apps_623_wf.wdl │ │ ├── dependency_report_extras.json │ │ ├── dependency_report_wf1.wdl │ │ ├── dependency_report_wf2.wdl │ │ └── string_int_concat.wdl │ ├── struct │ │ ├── DEVEX-1196-struct-resolution-wrong-order │ │ │ ├── file1.wdl │ │ │ ├── file2.wdl │ │ │ └── file3.wdl │ │ ├── Person.wdl │ │ ├── Person_input.json │ │ ├── apps_1381_ori.wdl │ │ ├── apps_1381_prime.wdl │ │ ├── array_of_structs.wdl │ │ ├── array_of_structs_input.json │ │ ├── many_structs.wdl │ │ ├── struct_deref.wdl │ │ ├── struct_field.wdl │ │ └── struct_imported_twice │ │ │ ├── file1.wdl │ │ │ ├── file2.wdl │ │ │ └── file3.wdl │ ├── subworkflows │ │ ├── check_route.wdl │ │ ├── ensure_trains.wdl │ │ ├── scatter_subworkflow_with_optional.wdl │ │ ├── trains.wdl │ │ ├── trains_input.json │ │ ├── trains_results.json │ │ └── trains_station.wdl │ ├── util │ │ ├── block_closure.wdl │ │ ├── block_with_three_calls.wdl │ │ ├── block_zero.wdl │ │ ├── empty_workflow.wdl │ │ ├── expression_after_call.wdl │ │ ├── inputs_used_as_outputs.wdl │ │ ├── missing_inputs_to_direct_call.wdl │ │ ├── nested_closure.wdl │ │ └── nested_closure_no_fw_ref.wdl │ ├── v1.1 │ │ └── add.wdl │ └── v2 │ │ ├── apps_1421_dir_output_unit.wdl │ │ ├── call_dnanexus_applet.wdl │ │ ├── dnanexus_applet.wdl │ │ ├── library.wdl │ │ └── movies.wdl │ └── scala │ └── dx │ ├── compiler │ ├── CompilerTest.scala │ └── ExecTreeTest.scala │ ├── dxni │ └── DxNativeInterfaceTest.scala │ ├── package.scala │ └── translator │ ├── CorporaTest.scala │ ├── ExtrasTest.scala │ ├── InputTranslatorTest.scala │ ├── TranslatorTest.scala │ ├── cwl │ └── ProcessTranslatorTest.scala │ └── wdl │ └── CallableTranslatorTest.scala ├── contrib ├── beginner_example │ ├── bam_chrom_counter.cwl │ ├── bam_chrom_counter.cwl.json │ ├── bam_chrom_counter.wdl │ ├── bam_chrom_counter_input.json │ ├── count_bam.cwl │ ├── cwl_v1.0 │ │ ├── bam_chrom_counter.cwl │ │ ├── count_bam.cwl │ │ └── slice_bam.cwl │ └── slice_bam.cwl ├── czi │ ├── README.md │ └── count │ │ ├── CountLines.wdl │ │ ├── WDL_INPUTS.org.json │ │ ├── count.orig.wdl │ │ ├── count.wdl │ │ └── inputs.json └── validate_bam │ └── validate-bam.wdl ├── core └── src │ ├── main │ ├── resources │ │ ├── application.conf │ │ └── logback.xml │ └── scala │ │ └── dx │ │ ├── core │ │ ├── CliUtils.scala │ │ ├── Constants.scala │ │ ├── io │ │ │ ├── DxWorkerPaths.scala │ │ │ ├── DxdaManifest.scala │ │ │ ├── DxfuseManifest.scala │ │ │ ├── DxuaManifest.scala │ │ │ └── package.scala │ │ ├── ir │ │ │ ├── Archive.scala │ │ │ ├── Block.scala │ │ │ ├── DxName.scala │ │ │ ├── ExecutableLink.scala │ │ │ ├── Manifest.scala │ │ │ ├── ParameterLink.scala │ │ │ ├── RunSpec.scala │ │ │ ├── SourceCode.scala │ │ │ ├── Type.scala │ │ │ ├── TypeSerde.scala │ │ │ ├── Value.scala │ │ │ ├── ValueSerde.scala │ │ │ └── package.scala │ │ ├── languages │ │ │ ├── Language.scala │ │ │ ├── cwl │ │ │ │ ├── CwlBlock.scala │ │ │ │ ├── CwlBundle.scala │ │ │ │ ├── CwlDxName.scala │ │ │ │ ├── CwlUtils.scala │ │ │ │ ├── DxHintSchema.scala │ │ │ │ ├── RequirementEvaluator.scala │ │ │ │ └── package.scala │ │ │ └── wdl │ │ │ │ ├── ArchiveFunction.scala │ │ │ │ ├── Runtime.scala │ │ │ │ ├── VersionSupport.scala │ │ │ │ ├── WdlBlock.scala │ │ │ │ ├── WdlBundle.scala │ │ │ │ ├── WdlCodeGenerator.scala │ │ │ │ ├── WdlDxName.scala │ │ │ │ └── WdlUtils.scala │ │ └── package.scala │ │ └── package.scala │ └── test │ ├── resources │ ├── block │ │ └── b1.wdl │ ├── bugs │ │ ├── apps-422.wdl │ │ ├── apps_384.wdl │ │ ├── apps_912_version_error_msg_fix.wdl │ │ ├── missing_chars_in_task.wdl │ │ ├── scatter_variable_not_found.wdl │ │ └── unpassed_argument_propagation.wdl │ ├── compiler │ │ ├── BroadGenomicsDocker.wdl │ │ ├── GPU.wdl │ │ ├── GPU2.wdl │ │ ├── Readme.wf_readme.add.md │ │ ├── Readme.wf_readme.wf_readme.md │ │ ├── add.wdl │ │ ├── add_app_meta.wdl │ │ ├── add_default.wdl │ │ ├── add_dx_type.wdl │ │ ├── add_group.wdl │ │ ├── add_help.wdl │ │ ├── add_label.wdl │ │ ├── add_runtime_hints.wdl │ │ ├── add_timeout.wdl │ │ ├── add_timeout_override.wdl │ │ ├── call_level2.wdl │ │ ├── cast.wdl │ │ ├── check_imports.wdl │ │ ├── choice_obj_values.wdl │ │ ├── choice_values.wdl │ │ ├── choices_type_mismatch.wdl │ │ ├── default_type_mismatch.wdl │ │ ├── dict.wdl │ │ ├── dict2.wdl │ │ ├── dx_type_nonfile.wdl │ │ ├── environment_passing_deep_nesting.wdl │ │ ├── expr_output_block.wdl │ │ ├── extras │ │ │ ├── extras_custom_reorg.json │ │ │ ├── extras_custom_reorg_config.json │ │ │ ├── extras_license.json │ │ │ ├── short_timeout.json │ │ │ └── task_specific_short_timeout.json │ │ ├── help_input_params.wdl │ │ ├── help_output_params.wdl │ │ ├── imports │ │ │ ├── A.wdl │ │ │ ├── A_inputs.json │ │ │ ├── lib.wdl │ │ │ ├── lib │ │ │ │ └── library.wdl │ │ │ └── subworkflow.wdl │ │ ├── instance_type_test.wdl │ │ ├── library.wdl │ │ ├── meta_section.wdl │ │ ├── multi_import.wdl │ │ ├── nested_scatter.wdl │ │ ├── optional_call_output.wdl │ │ ├── optionals.wdl │ │ ├── pattern_obj_params.wdl │ │ ├── pattern_params.wdl │ │ ├── reserved.wdl │ │ ├── scatter_no_call.wdl │ │ ├── scatter_subworkflow_with_optional.wdl │ │ ├── streaming_files.wdl │ │ ├── streaming_files_error1.wdl │ │ ├── streaming_files_error2.wdl │ │ ├── streaming_files_obj.wdl │ │ ├── strings.wdl │ │ ├── subblock_several_calls.wdl │ │ ├── suggestion_obj_values.wdl │ │ ├── suggestion_values.wdl │ │ ├── suggestions_missing_arg.wdl │ │ ├── suggestions_type_mismatch.wdl │ │ ├── wf_constants.wdl │ │ ├── wf_custom_reorg.wdl │ │ ├── wf_linear.wdl │ │ ├── wf_linear_no_expr.wdl │ │ ├── wf_meta.wdl │ │ ├── wf_param_meta.wdl │ │ ├── wf_readme.wdl │ │ ├── wf_to_flatten.wdl │ │ └── wf_with_output_expressions.wdl │ ├── draft2 │ │ ├── block_category.wdl │ │ ├── block_closure.wdl │ │ ├── conditionals1.wdl │ │ ├── conditionals2.wdl │ │ ├── conditionals3.wdl │ │ ├── conditionals4.wdl │ │ ├── conditionals_base.wdl │ │ ├── library.wdl │ │ ├── library_math.wdl │ │ ├── movies.wdl │ │ ├── pair.wdl │ │ ├── shapes.wdl │ │ ├── streaming.wdl │ │ └── various_calls.wdl │ ├── logback-test.xml │ ├── nested │ │ ├── extras │ │ │ ├── four_levels_extras1.json │ │ │ └── four_levels_extras2.json │ │ ├── four_levels.wdl │ │ ├── four_levels_input.json │ │ ├── param_passing.wdl │ │ ├── three_levels.wdl │ │ ├── three_levels_input.json │ │ └── two_levels.wdl │ ├── struct │ │ ├── DEVEX-1196-struct-resolution-wrong-order │ │ │ ├── file1.wdl │ │ │ ├── file2.wdl │ │ │ └── file3.wdl │ │ ├── Person.wdl │ │ ├── Person_input.json │ │ ├── array_of_structs.wdl │ │ ├── array_of_structs_input.json │ │ ├── many_structs.wdl │ │ └── struct_imported_twice │ │ │ ├── file1.wdl │ │ │ ├── file2.wdl │ │ │ └── file3.wdl │ ├── subworkflows │ │ ├── check_route.wdl │ │ ├── ensure_trains.wdl │ │ ├── scatter_subworkflow_with_optional.wdl │ │ ├── trains.wdl │ │ ├── trains_input.json │ │ ├── trains_results.json │ │ └── trains_station.wdl │ ├── util │ │ ├── block_closure.wdl │ │ ├── block_with_three_calls.wdl │ │ ├── block_zero.wdl │ │ ├── empty_workflow.wdl │ │ ├── expression_after_call.wdl │ │ ├── inputs_used_as_outputs.wdl │ │ ├── missing_inputs_to_direct_call.wdl │ │ ├── nested_closure.wdl │ │ └── nested_closure_no_fw_ref.wdl │ └── v2 │ │ ├── call_dnanexus_applet.wdl │ │ ├── dnanexus_applet.wdl │ │ ├── library.wdl │ │ └── movies.wdl │ └── scala │ └── dx │ └── core │ ├── io │ ├── DxFileAccessProtocolTest.scala │ ├── DxdaManifestTest.scala │ └── DxfuseManifestTest.scala │ ├── ir │ ├── ArchiveTest.scala │ ├── DxNameTest.scala │ ├── ManifestTest.scala │ ├── ParameterLinkTest.scala │ ├── TypeSerializationTest.scala │ └── ValueSerializationTest.scala │ ├── languages │ ├── LanguageTest.scala │ └── wdl │ │ ├── ArchiveFunctionTest.scala │ │ ├── InstanceTypesTest.scala │ │ ├── VersionSupportTest.scala │ │ ├── WdlBlockTest.scala │ │ └── WdlUtilsTest.scala │ └── package.scala ├── cwl_runner ├── CHANGELOG.md ├── README.md ├── dx_cwl_runner │ ├── __init__.py │ ├── arg_parser.py │ ├── compiler.py │ ├── cwl_runner.py │ ├── dx.py │ └── utils.py ├── poetry.lock └── pyproject.toml ├── doc ├── CWL_v1.2.0_to_WDL_v1.md ├── CustomReorgAppletExample.md ├── Debugging.md ├── Developing.md ├── ExpertOptions.md ├── FAQ.md ├── Internals.md ├── MissingCallArguments.md ├── TestCompilerInYourEnvironment.md ├── Tips.md ├── bam_chrom_counter.png ├── demo │ ├── demo.md │ └── hello_world.wdl ├── docker │ ├── Dockerfile │ └── Makefile ├── examples │ ├── four_levels.exectree.json │ └── four_levels.exectree.pretty.txt └── images │ ├── Makefile │ ├── linear.gv │ ├── linear.png │ ├── linear2.gv │ ├── linear2.png │ ├── mul-loop.png │ ├── mul_loop.gv │ ├── mul_loop.png │ ├── optionals.gv │ ├── optionals.png │ ├── two_levels.gv │ └── two_levels.png ├── dxcint ├── .editorconfig ├── .flake8 ├── DXCINT_UPDATES.md ├── README.md ├── config │ ├── cwl_cromwell.json │ ├── cwl_tools.json │ ├── cwl_workflows.json │ ├── large.json │ ├── medium.json │ ├── uncategorized.json │ └── wdl_cromwell.json ├── dependencies │ ├── applets │ │ ├── functional_reorg_test │ │ │ ├── code.py │ │ │ └── dxapp.json │ │ ├── native_concat │ │ │ ├── code.py │ │ │ └── dxapp.json │ │ ├── native_diff │ │ │ ├── code.sh │ │ │ └── dxapp.json │ │ ├── native_mk_list │ │ │ ├── code.py │ │ │ └── dxapp.json │ │ ├── native_sum │ │ │ ├── code.py │ │ │ └── dxapp.json │ │ └── native_sum_012 │ │ │ ├── code.py │ │ │ └── dxapp.json │ └── config │ │ ├── awscli.json │ │ ├── cwltool.json │ │ ├── dxda.json │ │ ├── dxfuse.json │ │ └── schema-salad.json ├── dxcint │ ├── Context.py │ ├── Dependency.py │ ├── Logger.py │ ├── Messenger.py │ ├── RegisteredTest.py │ ├── RegisteredTestFactory.py │ ├── Terraform.py │ ├── TestDiscovery.py │ ├── __init__.py │ ├── cli.py │ ├── constants.py │ ├── mixins │ │ ├── ExtrasMixin.py │ │ ├── JobCollectorMixin.py │ │ ├── ManifestMixin.py │ │ ├── PinnedInstanceMixin.py │ │ ├── ReorgMixin.py │ │ ├── ResultsTestMixin.py │ │ ├── StaticOnlyMixin.py │ │ ├── UnlockedMixin.py │ │ └── __init__.py │ ├── testclasses │ │ ├── AnalysisFinished.py │ │ ├── AppExternExpectedOutput.py │ │ ├── ExpectedFailure.py │ │ ├── ExpectedFailureMessage.py │ │ ├── ExpectedFlags.py │ │ ├── ExpectedOutput.py │ │ ├── ExternExpectedOutput.py │ │ ├── ExtrasAnalysisFinished.py │ │ ├── ExtrasExpectedFlags.py │ │ ├── ExtrasExpectedOutput.py │ │ ├── ManifestAnalysisFinished.py │ │ ├── ReorgExpectedOutput.py │ │ ├── StaticPinnedInstanceExpectedFailure.py │ │ ├── StaticPinnedInstanceExpectedOutput.py │ │ ├── UnlockedExpectedOutput.py │ │ ├── UnlockedExtrasExpectedOutput.py │ │ └── __init__.py │ └── utils.py ├── poetry.lock ├── pyproject.toml ├── resources │ ├── analysis_finished │ │ ├── DiskSpace2.wdl │ │ ├── DiskSpace2_input.json │ │ ├── a.wdl │ │ ├── aliased_subworkflows.wdl │ │ ├── apps_1052_optional_compound_input_wdl10.wdl │ │ ├── apps_1052_optional_compound_input_wdl10_input.json │ │ ├── apps_1318_nested.wdl │ │ ├── apps_384.wdl │ │ ├── apps_847_scatter_empty.wdl │ │ ├── apps_847_scatter_empty_input.json │ │ ├── apps_864.wdl │ │ ├── apps_864_input.json │ │ ├── apps_936.wdl │ │ ├── apps_936_input.json │ │ ├── apps_956_private_var_local.wdl │ │ ├── array_io.wdl │ │ ├── array_literal_locations.wdl │ │ ├── arrays_scatters_ifs.wdl │ │ ├── b.wdl │ │ ├── broad_genomics.wdl │ │ ├── bwa_mem.wdl │ │ ├── bwa_mem_input.json │ │ ├── c.wdl │ │ ├── cacheBetweenWF.wdl │ │ ├── cacheWithinWF.wdl │ │ ├── cached_copy.wdl │ │ ├── call_level2.wdl │ │ ├── call_level2_input.json │ │ ├── coerce_to_array_of_optionals.wdl │ │ ├── collections_delete.wdl │ │ ├── complex_types_files.wdl │ │ ├── continue_on_return_code.wdl │ │ ├── control_chars.wdl │ │ ├── cromwell_restart.wdl │ │ ├── curl.wdl │ │ ├── d.wdl │ │ ├── declarations_as_nodes.wdl │ │ ├── declarations_in_ifs.wdl │ │ ├── defined_function.wdl │ │ ├── diff_stream_and_download.wdl │ │ ├── diff_stream_and_download_input.json │ │ ├── docker_hash_gcr.wdl │ │ ├── docker_hash_quay.wdl │ │ ├── dollars_in_strings.wdl │ │ ├── dont_strip_line_prefix.wdl │ │ ├── dontglobinputs.wdl │ │ ├── dot_dir_stuck_running.wdl │ │ ├── download_from_container.wdl │ │ ├── empty_scatter.wdl │ │ ├── engine_functions.wdl │ │ ├── error_10_preemptible.wdl │ │ ├── exhaustive_delete.wdl │ │ ├── exit.wdl │ │ ├── filearrayoutput.wdl │ │ ├── final_call_logs_dir.wdl │ │ ├── floating_tags.wdl │ │ ├── forkjoin.wdl │ │ ├── forkjoin_input.json │ │ ├── globbingindex.wdl │ │ ├── globbingscatter.wdl │ │ ├── hello_delete.wdl │ │ ├── if_then_else_expressions.wdl │ │ ├── ifs_in_scatters.wdl │ │ ├── ifs_upstream_and_downstream.wdl │ │ ├── importer_ok.wdl │ │ ├── input_localization.wdl │ │ ├── input_mirror.wdl │ │ ├── inputs_provided_optional.wdl │ │ ├── inputs_provided_optional_input.json │ │ ├── jes_labels.wdl │ │ ├── length.wdl │ │ ├── local_gcs.wdl │ │ ├── localization_sanity_papi_v2.wdl │ │ ├── lots_of_inputs.wdl │ │ ├── lots_of_inputs_input.json │ │ ├── lots_of_nesting.wdl │ │ ├── map_file_key.wdl │ │ ├── map_file_key_input.json │ │ ├── map_workflow.wdl │ │ ├── member_access.wdl │ │ ├── memory_units.wdl │ │ ├── multiplesourcedarray.wdl │ │ ├── nested_lookups.inputs.json │ │ ├── nested_lookups.wdl │ │ ├── no_cache_delete.wdl │ │ ├── no_output_delete.wdl │ │ ├── no_task_no_output_delete.wdl │ │ ├── non_root_default_user.wdl │ │ ├── null_input_values.wdl │ │ ├── null_input_values_input.json │ │ ├── opt_array.wdl │ │ ├── opt_array_input.json │ │ ├── optional_missing.wdl │ │ ├── optional_missing_input.json │ │ ├── optional_output.wdl │ │ ├── postfix_quantifiers.wdl │ │ ├── prefix.wdl │ │ ├── prepare_scatter_gather.wdl │ │ ├── public_http_import.wdl │ │ ├── readFromCache.wdl │ │ ├── read_tsv.wdl │ │ ├── read_write_json_roundtrip.wdl │ │ ├── read_write_json_roundtrip_develop.wdl │ │ ├── read_write_map.wdl │ │ ├── recimp_nosubwf_inner.wdl │ │ ├── recimp_nosubwf_outer.wdl │ │ ├── referencingpreviousinputsandoutputs.wdl │ │ ├── samtools_count.wdl │ │ ├── samtools_count_input.json │ │ ├── scatter.wdl │ │ ├── scatter_chain.wdl │ │ ├── scatter_delete.wdl │ │ ├── scatter_subworkflow_with_optional.wdl │ │ ├── scattered.wdl │ │ ├── scattergather.wdl │ │ ├── scatters_in_ifs.wdl │ │ ├── select_functions.wdl │ │ ├── simple_if.wdl │ │ ├── simple_scatter.wdl │ │ ├── sizerelativepath.wdl │ │ ├── sort_file.wdl │ │ ├── sort_file_input.json │ │ ├── space.wdl │ │ ├── spaces_in_file_paths.wdl │ │ ├── square.wdl │ │ ├── stdout_delete.wdl │ │ ├── stdout_stderr_passing.wdl │ │ ├── struct_deref.wdl │ │ ├── struct_deref_input.json │ │ ├── sub_function.wdl │ │ ├── sub_sub_sub.wdl │ │ ├── sub_workflow_delete.wdl │ │ ├── sub_workflow_delete_import.wdl │ │ ├── sub_workflow_interactions_scatter.wdl │ │ ├── sub_workflow_no_output_block_import.wdl │ │ ├── sub_workflow_no_outputs_in_block_import.wdl │ │ ├── sub_workflow_one_output_import.wdl │ │ ├── sub_workflow_var_refs.wdl │ │ ├── sub_workflow_var_refs_import.wdl │ │ ├── subdirectory.wdl │ │ ├── subworkflow_wt.wdl │ │ ├── subworkflow_wt_input.json │ │ ├── subworkflows_in_ifs.wdl │ │ ├── symlink_localization.wdl │ │ ├── top_wf.wdl │ │ ├── top_wf_input.json │ │ ├── unpassed_default_arg.wdl │ │ ├── unzip_files.wdl │ │ ├── unzip_files_input.json │ │ ├── use_cacheCopy_dir.wdl │ │ ├── variable_scoping.wdl │ │ ├── volatile_disables_cache.wdl │ │ ├── wdl_empty_glob.wdl │ │ ├── wdl_function_locations.wdl │ │ ├── workflow_name_length_ok.wdl │ │ ├── workflow_output_declarations.wdl │ │ ├── workflow_output_paths.wdl │ │ ├── workflow_output_paths_colliding.wdl │ │ ├── workflow_type_and_version_wdl.wdl │ │ ├── workflowenginefunctions.wdl │ │ ├── writeToCache.wdl │ │ ├── write_lines.wdl │ │ ├── write_lines_files.wdl │ │ └── write_tsv.wdl │ ├── app_extern_expected_output │ │ ├── call_native_app.wdl │ │ ├── call_native_app_input.json │ │ └── call_native_app_results.json │ ├── expected_failure │ │ ├── apps_1014.wdl │ │ ├── argument_list_too_long.wdl │ │ ├── bad_status.wdl │ │ ├── bad_status2.wdl │ │ ├── docker_retry.wdl │ │ └── just_fail_wf.wdl │ ├── expected_failure_message │ │ ├── python_task_fail.wdl │ │ ├── python_task_fail_docker.wdl │ │ ├── python_task_fail_docker_results.json │ │ └── python_task_fail_results.json │ ├── expected_flags │ │ ├── add2.wdl │ │ ├── add2_extras.json │ │ ├── add2_input.json │ │ ├── add2_results.json │ │ ├── apps_1647_dx_restart.wdl │ │ └── apps_1647_dx_restart_results.json │ ├── expected_output │ │ ├── add3.wdl │ │ ├── add3_input.json │ │ ├── add3_results.json │ │ ├── advanced.wdl │ │ ├── advanced_input.json │ │ ├── advanced_results.json │ │ ├── apps_1052_optional_block_inputs_wdl10.wdl │ │ ├── apps_1052_optional_block_inputs_wdl10_results.json │ │ ├── apps_1052_optional_block_inputs_wdl11.wdl │ │ ├── apps_1052_optional_block_inputs_wdl11_results.json │ │ ├── apps_378.wdl │ │ ├── apps_378_input.json │ │ ├── apps_378_results.json │ │ ├── apps_573.wdl │ │ ├── apps_573_results.json │ │ ├── apps_579_boolean_flag_expr.wdl │ │ ├── apps_579_boolean_flag_expr_results.json │ │ ├── apps_579_string_substitution_expr.wdl │ │ ├── apps_579_string_substitution_expr_results.json │ │ ├── apps_612.wdl │ │ ├── apps_612_input.json │ │ ├── apps_612_results.json │ │ ├── apps_700.wdl │ │ ├── apps_700_input.json │ │ ├── apps_700_results.json │ │ ├── call_with_defaults2.wdl │ │ ├── call_with_defaults2_input.json │ │ ├── call_with_defaults2_results.json │ │ ├── checkpointing.wdl │ │ ├── checkpointing_results.json │ │ ├── conditionals2.wdl │ │ ├── conditionals2_input.json │ │ ├── conditionals2_results.json │ │ ├── conditionals_base.wdl │ │ ├── conditionals_base_input.json │ │ ├── conditionals_base_results.json │ │ ├── custom_entrypoint.wdl │ │ ├── custom_entrypoint_results.json │ │ ├── diff2files.wdl │ │ ├── diff2files_input.json │ │ ├── diff2files_results.json │ │ ├── docker_image_cache_false.wdl │ │ ├── docker_image_cache_false_results.json │ │ ├── docker_image_cache_unspecified.wdl │ │ ├── docker_image_cache_unspecified_results.json │ │ ├── dynamic_docker_image.wdl │ │ ├── dynamic_docker_image_input.json │ │ ├── dynamic_docker_image_results.json │ │ ├── echo_line_split.wdl │ │ ├── echo_line_split_results.json │ │ ├── echo_pairs.wdl │ │ ├── echo_pairs_input.json │ │ ├── echo_pairs_results.json │ │ ├── empty_array.wdl │ │ ├── empty_array_input.json │ │ ├── empty_array_results.json │ │ ├── empty_stdout.wdl │ │ ├── empty_stdout_results.json │ │ ├── empty_string.wdl │ │ ├── empty_string_results.json │ │ ├── environment_passing_deep_nesting.wdl │ │ ├── environment_passing_deep_nesting_input.json │ │ ├── environment_passing_deep_nesting_results.json │ │ ├── file_evaluator_identifier_lookups.wdl │ │ ├── file_evaluator_identifier_lookups_results.json │ │ ├── file_outputs_from_input.wdl │ │ ├── file_outputs_from_input_results.json │ │ ├── files_with_the_same_name.wdl │ │ ├── files_with_the_same_name_input.json │ │ ├── files_with_the_same_name_results.json │ │ ├── four_levels.wdl │ │ ├── four_levels_input.json │ │ ├── four_levels_results.json │ │ ├── linear.wdl │ │ ├── linear_no_expressions.wdl │ │ ├── linear_no_expressions_results.json │ │ ├── linear_results.json │ │ ├── missing_optional_output_file.wdl │ │ ├── missing_optional_output_file_results.json │ │ ├── modulo.wdl │ │ ├── modulo_input.json │ │ ├── modulo_results.json │ │ ├── movies.wdl │ │ ├── movies_input.json │ │ ├── movies_results.json │ │ ├── multiline_command_line.wdl │ │ ├── multiline_command_line_results.json │ │ ├── multiple_imports.wdl │ │ ├── multiple_imports_input.json │ │ ├── multiple_imports_results.json │ │ ├── native_docker_file_image.wdl │ │ ├── native_docker_file_image_gzip.wdl │ │ ├── native_docker_file_image_gzip_results.json │ │ ├── native_docker_file_image_results.json │ │ ├── nested_optional.wdl │ │ ├── nested_optional_input.json │ │ ├── nested_optional_results.json │ │ ├── nested_pairs.wdl │ │ ├── nested_pairs_input.json │ │ ├── nested_pairs_results.json │ │ ├── nested_scatter.wdl │ │ ├── nested_scatter_results.json │ │ ├── optionals3.wdl │ │ ├── optionals3_input.json │ │ ├── optionals3_results.json │ │ ├── outer.wdl │ │ ├── outer_input.json │ │ ├── outer_results.json │ │ ├── output_filename_interpolation.wdl │ │ ├── output_filename_interpolation_results.json │ │ ├── output_redirection.wdl │ │ ├── output_redirection_results.json │ │ ├── param_passing.wdl │ │ ├── param_passing_input.json │ │ ├── param_passing_results.json │ │ ├── passingfiles.wdl │ │ ├── passingfiles_results.json │ │ ├── runtime_vs_static_type.wdl │ │ ├── runtime_vs_static_type_result.json │ │ ├── simple_if_workflow_outputs.wdl │ │ ├── simple_if_workflow_outputs_results.json │ │ ├── single_to_array_conversion.wdl │ │ ├── single_to_array_conversion_results.json │ │ ├── stream_diff_v1.wdl │ │ ├── stream_diff_v1_input.json │ │ ├── stream_diff_v1_results.json │ │ ├── streaming_inputs.wdl │ │ ├── streaming_inputs_input.json │ │ ├── streaming_inputs_results.json │ │ ├── sub_workflow_decls.wdl │ │ ├── sub_workflow_decls_input.json │ │ ├── sub_workflow_decls_results.json │ │ ├── sub_workflow_hello_world.wdl │ │ ├── sub_workflow_hello_world_results.json │ │ ├── subblocks.wdl │ │ ├── subblocks2.wdl │ │ ├── subblocks2_input.json │ │ ├── subblocks2_results.json │ │ ├── subblocks_input.json │ │ ├── subblocks_results.json │ │ ├── subworkflow_with_task.wdl │ │ ├── subworkflow_with_task_results.json │ │ ├── three_levels.wdl │ │ ├── three_levels_input.json │ │ ├── three_levels_results.json │ │ ├── two_levels.wdl │ │ ├── two_levels_results.json │ │ ├── upload_workflow_files.wdl │ │ ├── upload_workflow_files_results.json │ │ ├── v1_1_dict.wdl │ │ ├── v1_1_dict_results.json │ │ ├── var_type_change.wdl │ │ ├── var_type_change_results.json │ │ ├── wf_person.wdl │ │ ├── wf_person_input.json │ │ ├── wf_person_results.json │ │ ├── wf_with_input_expressions.wdl │ │ ├── wf_with_input_expressions_input.json │ │ ├── wf_with_input_expressions_results.json │ │ ├── wf_with_output_expressions.wdl │ │ ├── wf_with_output_expressions_input.json │ │ ├── wf_with_output_expressions_results.json │ │ ├── workflow_engine_functions.wdl │ │ ├── workflow_engine_functions_results.json │ │ ├── workflow_with_subworkflow.wdl │ │ ├── workflow_with_subworkflow_results.json │ │ ├── write_lines_bug.wdl │ │ ├── write_lines_bug_input.json │ │ └── write_lines_bug_results.json │ ├── extern_expected_output │ │ ├── call_native_v1.wdl │ │ ├── call_native_v1_input.json │ │ └── call_native_v1_results.json │ ├── extras_analysis_finished │ │ ├── biocontainers.wdl │ │ ├── biocontainers_extras.json │ │ ├── ecr_docker.wdl │ │ ├── ecr_docker_extras.json │ │ └── ecr_docker_input.json │ ├── extras_expected_flags │ │ ├── apps_2478_headJobOnDemand_subjob.wdl │ │ ├── apps_2478_headJobOnDemand_subjob_extras.json │ │ ├── apps_2478_headJobOnDemand_subjob_input.json │ │ └── apps_2478_headJobOnDemand_subjob_results.json │ ├── extras_expected_output │ │ ├── instance_types.wdl │ │ ├── instance_types_extras.json │ │ ├── instance_types_input.json │ │ ├── instance_types_results.json │ │ ├── private_registry.wdl │ │ ├── private_registry_extras.json │ │ ├── private_registry_results.json │ │ ├── symlinks_wc.wdl │ │ ├── symlinks_wc_extras.json │ │ ├── symlinks_wc_input.json │ │ └── symlinks_wc_results.json │ ├── imports │ │ ├── array_add.wdl │ │ ├── array_mul.wdl │ │ ├── bag_of_tasks.wdl │ │ ├── inner.wdl │ │ ├── library.wdl │ │ ├── library_math.wdl │ │ ├── library_string.wdl │ │ ├── library_sys_call.wdl │ │ ├── nested_wf.wdl │ │ ├── scatter_if.wdl │ │ ├── structs.wdl │ │ ├── sub_workflow_decls_import.wdl │ │ ├── sub_workflow_hello_world_import.wdl │ │ ├── sub_workflow_interactions_import.wdl │ │ ├── subworkflow_ii.wdl │ │ ├── subworkflow_with_defaults.wdl │ │ ├── test_task.wdl │ │ └── tumor_normal.wdl │ ├── manifest_analysis_finished │ │ ├── apps_1269_1270_unqualified_ids_manifest.wdl │ │ ├── apps_1269_1270_unqualified_ids_manifest_input.json │ │ ├── complex_manifest.wdl │ │ ├── complex_manifest_input.json │ │ ├── simple_manifest.wdl │ │ ├── simple_manifest_input.json │ │ ├── view_and_count_manifest.wdl │ │ └── view_and_count_manifest_input.json │ ├── reorg_expected_output │ │ ├── dict.wdl │ │ ├── dict_results.json │ │ ├── strings.wdl │ │ └── strings_results.json │ ├── static_pinned_instance_expected_failure │ │ ├── diskspace_exhauster.wdl │ │ └── diskspace_exhauster_input.json │ ├── static_pinned_instance_expected_output │ │ ├── apps_1128_frag_native_instance_type_override.wdl │ │ ├── apps_1128_frag_native_instance_type_override_results.json │ │ ├── apps_1177_native_indirect_override.wdl │ │ ├── apps_1177_native_indirect_override_results.json │ │ ├── apps_1197_native_frag_default.wdl │ │ └── apps_1197_native_frag_default_results.json │ ├── unlocked_expected_output │ │ ├── array_structs.wdl │ │ ├── array_structs_input.json │ │ ├── array_structs_results.json │ │ ├── call_with_defaults1.wdl │ │ ├── call_with_defaults1_input.json │ │ ├── call_with_defaults1_results.json │ │ ├── cast.wdl │ │ ├── cast_input.json │ │ ├── cast_results.json │ │ ├── files.wdl │ │ ├── files_input.json │ │ ├── files_results.json │ │ ├── optionals.wdl │ │ ├── optionals_input.json │ │ ├── optionals_results.json │ │ ├── shapes.wdl │ │ ├── shapes_input.json │ │ └── shapes_result.json │ └── unlocked_extras_expected_output │ │ ├── hello.wdl │ │ ├── hello_extras.json │ │ └── hello_results.json └── tests │ ├── __init__.py │ ├── conftest.py │ ├── fixtures │ ├── config │ │ └── medium.json │ ├── dependencies │ │ └── config │ │ │ ├── mock_dependency.json │ │ │ ├── mock_dependency_src.json │ │ │ └── mock_dependency_tar.json │ ├── mocker │ │ ├── mock_analysis.json │ │ └── mock_analysis_unlocked.json │ ├── new_tests │ │ └── mock_test.wdl │ └── resources │ │ └── mock_category │ │ ├── efm.wdl │ │ ├── efm_results.json │ │ ├── mock_1.wdl │ │ ├── mock_1_extras.json │ │ ├── mock_1_flags_results.json │ │ ├── mock_1_input.json │ │ ├── mock_1_results.json │ │ └── mock_2.cwl │ ├── mixins │ ├── __init__.py │ ├── test_ExtrasMixin.py │ ├── test_JobCollectorMixin.py │ ├── test_ManifestMixin.py │ ├── test_PinnedInstanceMixin.py │ ├── test_ReorgMixin.py │ ├── test_StaticOnlyMixin.py │ ├── test_UnlockedMixin.py │ └── test_supermixer.py │ ├── test_Context.py │ ├── test_Dependency.py │ ├── test_Messenger.py │ ├── test_RegisteredTest.py │ ├── test_Terraform.py │ ├── test_TestDiscovery.py │ ├── test_util.py │ └── testclasses │ ├── __init__.py │ ├── test_AnalysisFinished.py │ ├── test_AppExternExpectedOutput.py │ ├── test_ExpectedFailure.py │ ├── test_ExpectedFailureMessage.py │ ├── test_ExpectedFlags.py │ ├── test_ExpectedOutput.py │ ├── test_ExternExpectedOutput.py │ └── test_UnlockedExpectedOutput.py ├── executorCommon └── src │ ├── main │ ├── resources │ │ ├── application.conf │ │ └── logback.xml │ └── scala │ │ └── dx │ │ └── executor │ │ ├── BaseCli.scala │ │ ├── JobMeta.scala │ │ ├── TaskExecutor.scala │ │ └── WorkflowExecutor.scala │ └── test │ └── scala │ └── dx │ └── executor │ └── package.scala ├── executorCwl ├── applet_resources │ └── Makefile └── src │ ├── main │ ├── resources │ │ ├── application.conf │ │ └── logback.xml │ └── scala │ │ ├── dx │ │ └── executor │ │ │ └── cwl │ │ │ ├── CwlTaskExecutor.scala │ │ │ └── CwlWorkflowExecutor.scala │ │ └── dxExecutorCwl │ │ └── Main.scala │ └── test │ ├── resources │ └── tool_executor │ │ ├── rec │ │ ├── A │ │ ├── B │ │ ├── C │ │ └── D │ │ ├── record-in-format.cwl.json │ │ ├── record-in-format_input.json │ │ ├── recursive-input-directory.cwl.json │ │ ├── recursive-input-directory_input.json │ │ └── recursive-input-directory_output.json │ └── scala │ └── dx │ └── executor │ └── cwl │ ├── CwlTaskExecutorTest.scala │ └── package.scala ├── executorWdl └── src │ ├── main │ ├── resources │ │ ├── application.conf │ │ └── logback.xml │ └── scala │ │ ├── dx │ │ └── executor │ │ │ └── wdl │ │ │ ├── WdlTaskExecutor.scala │ │ │ ├── WdlWorkflowExecutor.scala │ │ │ └── package.scala │ │ └── dxExecutorWdl │ │ └── Main.scala │ └── test │ ├── resources │ ├── bugs │ │ ├── missing_chars_in_task.wdl │ │ ├── opt_with_default.wdl │ │ ├── scatter_variable_not_found.wdl │ │ └── unpassed_argument_propagation.wdl │ ├── draft2 │ │ ├── block_category.wdl │ │ ├── block_closure.wdl │ │ ├── conditionals1.wdl │ │ ├── conditionals2.wdl │ │ ├── conditionals3.wdl │ │ ├── conditionals4.wdl │ │ ├── conditionals_base.wdl │ │ ├── library.wdl │ │ ├── library_math.wdl │ │ ├── movies.wdl │ │ ├── pair.wdl │ │ ├── shapes.wdl │ │ ├── streaming.wdl │ │ └── various_calls.wdl │ ├── frag_runner │ │ ├── House.wdl │ │ ├── apps_1341.wdl │ │ ├── apps_1422_deref_out.wdl │ │ ├── conditional_no_call.wdl │ │ ├── ma.json │ │ ├── missing_args.wdl │ │ ├── nested_no_call.wdl │ │ ├── scatter_no_call.wdl │ │ ├── scatter_variable_not_found.wdl │ │ ├── scatter_with_eval.wdl │ │ ├── strings.wdl │ │ └── wf_linear.wdl │ ├── logback-test.xml │ ├── nested │ │ ├── extras │ │ │ ├── four_levels_extras1.json │ │ │ └── four_levels_extras2.json │ │ ├── four_levels.wdl │ │ ├── four_levels_input.json │ │ ├── param_passing.wdl │ │ ├── three_levels.wdl │ │ ├── three_levels_input.json │ │ └── two_levels.wdl │ └── task_runner │ │ ├── Person2.wdl │ │ ├── Person2_input.json │ │ ├── Person2_output.json │ │ ├── add.wdl │ │ ├── add_input.json │ │ ├── add_output.json │ │ ├── array_output.wdl │ │ ├── cast.wdl │ │ ├── cast_input.json │ │ ├── cast_output.json │ │ ├── cgrep.wdl │ │ ├── cgrep_input.json │ │ ├── cgrep_output.json │ │ ├── create_tsv_output.json │ │ ├── empty_command_section.wdl │ │ ├── empty_command_section_input.json │ │ ├── expressions_runtime_section.wdl │ │ ├── expressions_runtime_section_2.wdl │ │ ├── expressions_runtime_section_2_input.json │ │ ├── expressions_runtime_section_2_output.json │ │ ├── expressions_runtime_section_input.json │ │ ├── expressions_runtime_section_output.json │ │ ├── float_arith.wdl │ │ ├── float_arith_input.json │ │ ├── float_arith_output.json │ │ ├── manuscript.txt │ │ ├── missing_optional_output_file.wdl │ │ ├── missing_optional_output_file_results.json │ │ ├── opt_array.wdl │ │ ├── opt_array_input.json │ │ ├── ps.wdl │ │ ├── python_heredoc.wdl │ │ ├── python_heredoc_input.json │ │ ├── read_tsv_x.wdl │ │ ├── read_tsv_x_input.json │ │ ├── spaces_in_file_paths.json │ │ ├── spaces_in_file_paths.wdl │ │ ├── sub.wdl │ │ ├── sub_input.json │ │ ├── sub_output.json │ │ ├── two_files.wdl │ │ ├── two_files_input.json │ │ └── write_tsv_x.wdl │ └── scala │ └── dx │ └── executor │ └── wdl │ ├── WdlTaskExecutorTest.scala │ ├── WdlWorkflowExecutorTest.scala │ └── package.scala ├── project ├── Merging.scala ├── build.properties └── plugins.sbt ├── scripts ├── Makefile ├── build_all_releases.sh ├── build_release.py ├── bundled_dependencies.json ├── clean_build.sh ├── docker_image │ ├── Dockerfile │ ├── README.md │ ├── docker.env │ ├── docker_build.sh │ ├── docker_run.sh │ └── test.sh ├── dxCompiler_projects_utils │ └── test_projects │ │ └── dxCompiler_test_projects_stg.txt ├── dxcompiler_copy │ ├── README.md │ ├── code.sh │ └── dxapp.json ├── extract_source_code.sh ├── mk_symlink.py ├── multi_region_tests.py ├── proxy_test.py ├── requirements.txt ├── run_multiuser_tests.py ├── run_tests.py ├── squid_allow_all.conf ├── squid_allow_authorized.conf ├── squid_disallow_all.conf ├── update_version.sh └── util.py └── test ├── .gitignore ├── applets ├── README.md ├── functional_reorg_test │ ├── code.py │ └── dxapp.json ├── native_concat │ ├── code.py │ └── dxapp.json ├── native_diff │ ├── code.sh │ └── dxapp.json ├── native_mk_list │ ├── code.py │ └── dxapp.json ├── native_sum │ ├── code.py │ └── dxapp.json └── native_sum_012 │ ├── code.py │ └── dxapp.json ├── apps └── native_hello │ ├── code.py │ └── dxapp.json ├── bugs ├── APPS-824 │ ├── scatter_over_files.wdl │ └── scatter_over_files_input.json ├── apps_1014.wdl ├── apps_1052_optional_block_inputs_wdl10.wdl ├── apps_1052_optional_block_inputs_wdl10_results.json ├── apps_1052_optional_block_inputs_wdl11.wdl ├── apps_1052_optional_block_inputs_wdl11_results.json ├── apps_1052_optional_compound_input_wdl10.wdl ├── apps_1052_optional_compound_input_wdl10_input.json ├── apps_1473_nested_arr.wdl ├── apps_378.wdl ├── apps_378_input.json ├── apps_378_results.json ├── apps_384.wdl ├── apps_573.wdl ├── apps_573_results.json ├── apps_579_boolean_flag_expr.wdl ├── apps_579_boolean_flag_expr_results.json ├── apps_579_string_substitution_expr.wdl ├── apps_579_string_substitution_expr_results.json ├── apps_700.wdl ├── apps_700_input.json ├── apps_700_results.json ├── apps_864.wdl ├── apps_864_input.json ├── apps_936.wdl ├── apps_936_input.json ├── apps_956_private_var_local.wdl ├── argument_list_too_long.wdl ├── diff_stream_and_download.wdl ├── diff_stream_and_download_input.json ├── diskspace_exhauster.wdl ├── diskspace_exhauster_input.json ├── nested_pairs.wdl ├── nested_pairs_input.json ├── nested_pairs_results.json ├── subworkflow_with_task.wdl ├── test_task.wdl ├── write_lines_bug.wdl ├── write_lines_bug_input.json └── write_lines_bug_results.json ├── cromwell ├── README.md ├── afters │ ├── afters.options.json │ ├── afters.wdl │ ├── afters_and_ifs.wdl │ └── afters_and_scatters.wdl ├── aliased_subworkflows │ ├── aliased_subworkflows.wdl │ ├── subworkflow_wt.wdl │ └── subworkflow_wt_input.json ├── array_io │ └── array_io.wdl ├── array_literal_locations │ └── array_literal_locations.wdl ├── arrays_scatters_ifs │ └── arrays_scatters_ifs.wdl ├── backendWithNoDocker │ └── backendWithNoDocker.wdl ├── cacheBetweenWF │ ├── cacheBetweenWF.options │ └── cacheBetweenWF.wdl ├── cacheWithinWF │ └── cacheWithinWF.wdl ├── cached_copy │ └── cached_copy.wdl ├── call_cache_capoeira │ ├── call_cache_capoeira_jes.wdl │ ├── call_cache_capoeira_local.wdl │ └── call_cache_capoeira_tes.wdl ├── call_cache_hit_prefixes │ ├── call_cache_hit_prefixes.wdl │ ├── call_cache_hit_prefixes_empty_hint.options │ ├── call_cache_hit_prefixes_empty_hint_input.json │ ├── call_cache_hit_prefixes_no_hint_input.json │ ├── call_cache_hit_prefixes_results.json │ ├── call_cache_hit_prefixes_two_roots_empty_hint_hit_papi_input.json │ ├── call_cache_hit_prefixes_two_roots_empty_hint_miss_papi_input.json │ ├── call_cache_hit_prefixes_two_roots_empty_hint_papi_first.options │ └── call_cache_hit_prefixes_two_roots_empty_hint_papi_second.options ├── checkpointing │ ├── checkpointing.wdl │ └── checkpointing_results.json ├── coerce_to_array_of_optionals │ └── coerce_to_array_of_optionals.wdl ├── complex_types_files │ └── complex_types_files.wdl ├── composedenginefunctions │ └── composedenginefunctions.wdl ├── conditionals_tests │ ├── declarations_in_ifs │ │ └── declarations_in_ifs.wdl │ ├── ifs_in_scatters │ │ └── ifs_in_scatters.wdl │ ├── ifs_upstream_and_downstream │ │ └── ifs_upstream_and_downstream.wdl │ ├── lots_of_nesting │ │ ├── lots_of_nesting.wdl │ │ └── scatter_if.wdl │ ├── nested_lookups │ │ ├── nested_lookups.inputs.json │ │ └── nested_lookups.wdl │ ├── scatters_in_ifs │ │ └── scatters_in_ifs.wdl │ ├── simple_if │ │ ├── simple_if.wdl │ │ └── simple_if_results.json │ ├── simple_if_workflow_outputs │ │ ├── simple_if_workflow_outputs.wdl │ │ └── simple_if_workflow_outputs_results.json │ └── subworkflows_in_ifs │ │ ├── subworkflow_ii.wdl │ │ └── subworkflows_in_ifs.wdl ├── confirm_preemptible │ ├── confirm_preemptible.wdl │ └── confirm_preemptible_results.json ├── continue_on_return_code │ └── continue_on_return_code.wdl ├── control_chars │ └── control_chars.wdl ├── copy_workflow_outputs │ ├── scattered.wdl │ ├── scattered_local.options │ ├── scattered_papi.options │ ├── unscattered.wdl │ ├── unscattered_local.options │ └── unscattered_papi.options ├── cromwell_restart │ └── cromwell_restart.wdl ├── cromwell_restart_papi_upgrade │ └── cromwell_restart_papi_upgrade.options ├── cromwell_utils.sh ├── curl │ └── curl.wdl ├── custom_cacheworthy_attributes │ └── custom_cacheworthy_attributes.wdl ├── custom_entrypoint │ ├── custom_entrypoint.wdl │ └── custom_entrypoint_results.json ├── custom_mount_point │ ├── custom_mount_point.options │ └── custom_mount_point.wdl ├── declarations │ ├── declarations.wdl │ └── declarations_input.json ├── declarations_as_nodes │ └── declarations_as_nodes.wdl ├── dedup_localizations_papi_v2 │ └── dedup_localizations_papi_v2.wdl ├── default_runtime_attributes │ ├── default_runtime_attributes.options │ ├── default_runtime_attributes.wdl │ └── default_runtime_attributes_results.json ├── defined_function │ └── defined_function.wdl ├── delete_intermediates │ ├── collections_delete.wdl │ ├── delete_intermediates.options │ ├── exhaustive_delete.wdl │ ├── hello_delete.wdl │ ├── missing_delete.wdl │ ├── no_cache_delete.wdl │ ├── no_output_delete.wdl │ ├── no_task_no_output_delete.wdl │ ├── scatter_delete.wdl │ ├── stdout_delete.wdl │ ├── sub_workflow_delete.wdl │ └── sub_workflow_delete_import.wdl ├── docker_alpine │ ├── docker_alpine.options │ └── docker_alpine.wdl ├── docker_hash │ ├── docker_hash.options │ ├── docker_hash_dockerhub.wdl │ ├── docker_hash_dockerhub_private.wdl │ ├── docker_hash_gcr.wdl │ ├── docker_hash_gcr_private.wdl │ └── docker_hash_quay.wdl ├── docker_image_cache │ ├── docker_image_cache_false.options.json │ ├── docker_image_cache_false.wdl │ ├── docker_image_cache_false_results.json │ ├── docker_image_cache_true.options.json │ ├── docker_image_cache_true.wdl │ ├── docker_image_cache_true_results.json │ ├── docker_image_cache_unspecified.options.json │ ├── docker_image_cache_unspecified.wdl │ └── docker_image_cache_unspecified_results.json ├── docker_size │ ├── docker_size_dockerhub.wdl │ └── docker_size_gcr.wdl ├── dollars_in_strings │ └── dollars_in_strings.wdl ├── dont_strip_line_prefix │ └── dont_strip_line_prefix.wdl ├── dontglobinputs │ └── dontglobinputs.wdl ├── dot_dir_stuck_running │ └── dot_dir_stuck_running.wdl ├── drs_tests │ ├── drs_usa_hca.wdl │ ├── drs_usa_hca_input.json │ ├── drs_usa_jdr.wdl │ └── drs_usa_jdr_input.json ├── dummy_scatter │ └── dummy_scatter.wdl ├── empty_scatter │ └── empty_scatter.wdl ├── empty_string │ ├── empty_string.wdl │ └── empty_string_results.json ├── error_10_preemptible │ └── error_10_preemptible.wdl ├── exit │ └── exit.wdl ├── file_evaluator_identifier_lookups │ ├── file_evaluator_identifier_lookups.wdl │ └── file_evaluator_identifier_lookups_results.json ├── file_name_too_long │ ├── a.wdl │ ├── b.wdl │ ├── c.wdl │ └── d.wdl ├── file_outputs_from_input │ ├── file_outputs_from_input.wdl │ └── file_outputs_from_input_results.json ├── filearrayoutput │ └── filearrayoutput.wdl ├── final_call_logs_dir │ ├── final_call_logs_dir.wdl │ ├── final_call_logs_dir_jes.options │ └── final_call_logs_dir_local.options ├── floating_tags │ ├── floating_tags.options │ └── floating_tags.wdl ├── fofn_caching │ └── fofn_caching.wdl ├── forkjoin │ ├── forkjoin.wdl │ └── forkjoin_input.json ├── gcs_file_name_with_newline_in_the_middle │ └── gcs_file_name_with_newline_in_the_middle.wdl ├── globbingBehavior │ └── globbingBehavior.wdl ├── globbingindex │ └── globbingindex.wdl ├── globbingscatter │ └── globbingscatter.wdl ├── hello_private_repo │ ├── hello_private_repo.inputs.json │ └── hello_private_repo.wdl ├── http_inputs │ ├── http_inputs │ ├── http_inputs.wdl │ └── http_inputs_input.json ├── if_then_else_expressions │ └── if_then_else_expressions.wdl ├── import_subdir │ ├── echo.wdl │ └── echo_task.wdl ├── input_expressions │ └── input_expressions.wdl ├── input_from_bucket_with_requester_pays │ ├── input_from_bucket_with_requester_pays.wdl │ └── input_from_bucket_with_requester_pays_input.json ├── input_localization │ ├── input_localization.options │ ├── input_localization.wdl │ └── localize_file_larger_than_disk_space.wdl ├── input_mirror │ └── input_mirror.wdl ├── inter_scatter_dependencies │ └── inter_scatter_dependencies.wdl ├── labels │ ├── invalid.labels │ ├── jes_labels.wdl │ └── valid.labels ├── large_final_workflow_outputs_dir │ ├── large_final_workflow_outputs_dir.options.json │ └── large_final_workflow_outputs_dir.wdl ├── length │ ├── length.wdl │ └── length_slurm_no_docker.options ├── local_backend │ ├── local_backend.options │ ├── local_backend.wdl │ └── local_backend_input.json ├── local_bourne │ └── local_bourne.wdl ├── local_gcs │ └── local_gcs.wdl ├── localization_sanity_papi_v2 │ └── localization_sanity_papi_v2.wdl ├── long_cmd │ └── long_cmd.wdl ├── lots_of_inputs │ ├── lots_of_inputs.wdl │ ├── lots_of_inputs_input.json │ └── lots_of_inputs_papiv2_input.json ├── map_workflow │ └── map_workflow.wdl ├── member_access │ └── member_access.wdl ├── memory_units │ └── memory_units.wdl ├── monitoring_image_script │ ├── monitoring_image_script.options.json │ ├── monitoring_image_script.wdl │ ├── monitoring_image_script_results.json │ └── monitoring_image_script_with_entrypoints.options.json ├── monitoring_log │ ├── monitoring_log.options │ └── monitoring_log.wdl ├── multiline_command_line │ ├── multiline_command_line.wdl │ └── multiline_command_line_results.json ├── multiplesourcedarray │ └── multiplesourcedarray.wdl ├── non_root_default_user │ ├── Dockerfile │ └── non_root_default_user.wdl ├── non_root_specified_user │ ├── non_root_specified_user.wdl │ └── non_root_specified_user_results.json ├── none_literal │ └── none_literal.wdl ├── null_input_values │ ├── null_input_values.wdl │ └── null_input_values_input.json ├── object_access │ └── object_access.wdl ├── optional_declarations │ ├── optional_declarations.wdl │ └── optional_declarations_input.json ├── optional_parameter │ ├── optional_parameter.wdl │ └── optional_parameter_input.json ├── output_filename_interpolation │ ├── output_filename_interpolation.wdl │ └── output_filename_interpolation_results.json ├── output_redirection │ ├── output_redirection.wdl │ └── output_redirection_results.json ├── papi_cpu_platform │ ├── papi_cpu_platform.wdl │ └── papi_cpu_platform_results.json ├── papi_v2_gcsa │ └── papi_v2_gcsa.wdl ├── papi_v2_log │ └── papi_v2_log.wdl ├── papi_v2_plain_detritus │ └── papi_v2_plain_detritus.wdl ├── parallel_composite_uploads │ ├── caching_off.options │ ├── parallel_composite_uploads_lib.wdl │ ├── parallel_composite_uploads_off.options │ ├── parallel_composite_uploads_off.wdl │ ├── parallel_composite_uploads_on.options │ └── parallel_composite_uploads_on.wdl ├── passingfiles │ ├── passingfiles.wdl │ └── passingfiles_results.json ├── postfix_quantifiers │ └── postfix_quantifiers.wdl ├── prefix │ ├── prefix.options │ └── prefix.wdl ├── public_http_import │ └── public_http_import.wdl ├── readFromCacheFalse │ ├── readFromCache.options │ └── readFromCache.wdl ├── read_tsv │ └── read_tsv.wdl ├── read_write_json │ ├── read_write_json.wdl │ ├── read_write_json_roundtrip.wdl │ └── read_write_json_roundtrip_develop.wdl ├── read_write_map │ └── read_write_map.wdl ├── recursive_imports │ ├── fjoin.wdl │ ├── hello_world.wdl │ ├── hello_world_import.wdl │ ├── recursive_imports.wdl │ ├── sub_interactions.wdl │ └── sub_interactions_import.wdl ├── recursive_imports_no_subwf │ ├── recimp_nosubwf_inner.wdl │ ├── recimp_nosubwf_outer.wdl │ └── recursive_imports_no_subwf.wdl ├── reference_disk │ ├── reference_disk_test.wdl │ ├── reference_disk_test_false.options.json │ ├── reference_disk_test_input.json │ ├── reference_disk_test_results.json │ ├── reference_disk_test_true.options.json │ └── reference_disk_test_unspecified.options.json ├── referencingpreviousinputsandoutputs │ └── referencingpreviousinputsandoutputs.wdl ├── relative_output_paths │ ├── options.json │ └── workflow_output_paths.wdl ├── requester_pays_gcs │ ├── engine_functions.options │ ├── engine_functions.wdl │ ├── engine_functions_negative.options │ ├── localization.options │ └── localization.wdl ├── results ├── runtime_attribute_expressions │ ├── runtime_attribute_expressions.wdl │ └── runtime_attribute_expressions_results.json ├── scatter_chain │ └── scatter_chain.wdl ├── scatter_simples │ ├── bag_of_tasks.wdl │ ├── nocallcache.options │ ├── prepare_scatter_gather.wdl │ ├── scatter.wdl │ ├── siblings_scatter.wdl │ └── simple_scatter.wdl ├── scattergather │ └── scattergather.wdl ├── search_outputs.py ├── select_functions │ └── select_functions.wdl ├── short_circuit │ └── short_circuit.wdl ├── simple_if │ └── simple_if.wdl ├── single_to_array_conversion │ ├── single_to_array_conversion.wdl │ └── single_to_array_conversion_results.json ├── sizerelativepath │ ├── 1495bytes.txt │ └── sizerelativepath.wdl ├── space │ └── space.wdl ├── square │ └── square.wdl ├── ssh_access │ ├── ssh_access.options.json │ └── ssh_access.wdl ├── standard_output_paths_colliding_prevented │ ├── options.json │ └── workflow_output_paths_colliding.wdl ├── stdout_stderr_passing │ └── stdout_stderr_passing.wdl ├── string_interpolation │ ├── string_interpolation.wdl │ └── string_interpolation_input.json ├── string_interpolation_optional │ ├── string_interpolation_optional.wdl │ └── string_interpolation_optional_results.json ├── sub_function │ └── sub_function.wdl ├── sub_sub │ ├── sub.wdl │ ├── sub_sub.wdl │ ├── sub_sub_sub.wdl │ └── top.wdl ├── sub_workflow_decls │ ├── sub_workflow_decls.wdl │ ├── sub_workflow_decls_import.wdl │ ├── sub_workflow_decls_input.json │ └── sub_workflow_decls_results.json ├── sub_workflow_hello_world │ ├── sub_workflow_hello_world.wdl │ ├── sub_workflow_hello_world_import.wdl │ └── sub_workflow_hello_world_results.json ├── sub_workflow_interactions │ ├── sub_workflow_interactions.wdl │ └── sub_workflow_interactions_import.wdl ├── sub_workflow_interactions_scatter │ ├── sub_workflow_interactions_import.wdl │ └── sub_workflow_interactions_scatter.wdl ├── sub_workflow_no_outputs │ ├── sub_workflow_no_output.wdl │ ├── sub_workflow_no_output_block_import.wdl │ ├── sub_workflow_no_outputs_in_block_import.wdl │ └── sub_workflow_one_output_import.wdl ├── sub_workflow_var_refs │ ├── sub_workflow_var_refs.wdl │ └── sub_workflow_var_refs_import.wdl ├── subdirectory │ └── subdirectory.wdl ├── super_massive_array_output │ └── super_massive_array_output.wdl ├── symlink_localization │ ├── symlink_localization.options │ └── symlink_localization.wdl ├── taskless_engine_functions │ └── taskless_engine_functions.wdl ├── tmp_dir │ └── tmp_dir.wdl ├── use_cacheCopy_dir │ └── use_cacheCopy_dir.wdl ├── variable_scoping │ └── variable_scoping.wdl ├── virtual_private_cloud │ ├── check_network_in_vpc.wdl │ └── wf_zone_options.json ├── volatile_disables_cache │ ├── volatile_disables_cache.options │ └── volatile_disables_cache.wdl ├── wdl_draft2 │ └── read_write_functions │ │ └── read_write_functions.wdl ├── wdl_empty_glob │ └── wdl_empty_glob.wdl ├── wdl_function_locations │ └── wdl_function_locations.wdl ├── wdl_optional_outputs │ ├── wdl_optional_outputs.wdl │ └── wdl_optional_outputs_unsupported.wdl ├── workbench_health_monitor_check │ └── workbench_health_monitor_check.wdl ├── workflow_engine_functions │ ├── workflow_engine_functions.wdl │ └── workflow_engine_functions_results.json ├── workflow_output_declarations │ └── workflow_output_declarations.wdl ├── workflow_type_and_version_wdl │ └── workflow_type_and_version_wdl.wdl ├── workflowenginefunctions │ └── workflowenginefunctions.wdl ├── writeToCache │ ├── writeToCache.options │ └── writeToCache.wdl ├── write_lines │ └── write_lines.wdl ├── write_lines_files │ └── write_lines_files.wdl └── write_tsv │ └── write_tsv.wdl ├── cromwell_failed ├── abort │ ├── instant_abort.wdl │ ├── scheduled_abort.options │ ├── scheduled_abort.wdl │ ├── sub_workflow_abort.wdl │ └── sub_workflow_aborted_import.wdl ├── attempt_to_call_size_function_on_bucket │ └── attempt_to_call_size_function_on_bucket.wdl ├── attempt_to_localize_bucket_as_file │ ├── attempt_to_localize_bucket_as_file.wdl │ ├── bucket_name_with_no_trailing_slash.json │ └── bucket_name_with_trailing_slash.json ├── bad_basename │ └── bad_basename.wdl ├── bad_docker_name │ └── bad_docker_name.wdl ├── bad_file_string │ └── bad_file_string.wdl ├── bad_output_task │ └── bad_output_task.wdl ├── bad_workflow_failure_mode │ ├── bad_workflow_failure_mode.options │ └── bad_workflow_failure_mode.wdl ├── chain_fail │ ├── chain_fail.wdl │ └── chain_fail_import.wdl ├── circular_dependencies │ └── circular_dependencies.wdl ├── cont_while_possible │ ├── cont_while_possible.options │ ├── cont_while_possible.wdl │ └── cont_while_possible_scatter.wdl ├── empty_filename │ ├── empty_filename.wdl │ └── oops.inputs.json ├── failing_continue_on_return_code │ └── failing_continue_on_return_code.wdl ├── failures │ ├── invalid_wdl │ │ └── invalid_wdl.wdl │ ├── restart_while_failing │ │ ├── restart_while_failing.options │ │ └── restart_while_failing.wdl │ └── terminal_status │ │ └── terminal_status.wdl ├── fast_fail_noAddress │ └── fast_fail_noAddress.wdl ├── import_passwd │ └── import_passwd.wdl ├── import_passwd_url │ └── import_passwd_url.wdl ├── invalid_inputs_json │ ├── empty_inputs_file_input.json │ ├── invalid_inputs_json.wdl │ ├── invalid_inputs_json_input.json │ └── invalid_inputs_json_object_input.json ├── invalid_return_code │ └── invalid_return_code.wdl ├── invalid_runtime_attributes │ └── invalid_runtime_attributes.wdl ├── invalid_use_reference_disks_specification │ ├── invalid_use_reference_disks_specification.options.json │ └── invalid_use_reference_disks_specification.wdl ├── labels_bad_workflow │ ├── badWorkflow.wdl │ └── badWorkflow_input.json ├── list_of_tests ├── max_retries │ ├── max_retries.options │ └── max_retries.wdl ├── missing_input_failure │ ├── missing_input_failure.wdl │ └── missing_input_failure_input.json ├── missing_sub_inputs │ ├── missing_sub_inputs.wdl │ ├── missing_sub_inputs_import.wdl │ └── missing_sub_inputs_input.json ├── monitoring_script_localization_failure │ ├── monitoring_script_localization_failure.options │ └── monitoring_script_localization_failure.wdl ├── no_new_calls │ ├── no_new_calls.options │ └── no_new_calls.wdl ├── papi_delocalization_required_files │ └── papi_delocalization_required_files.wdl ├── papi_fail_on_bad_attrs │ └── papi_fail_on_bad_attrs.wdl ├── papi_preemptible_and_max_retries │ └── papi_preemptible_and_max_retries.wdl ├── read_file_limits │ ├── read_file_limits.options │ └── read_file_limits.wdl ├── relative_output_paths_colliding │ ├── options.json │ └── workflow_output_paths_colliding.wdl ├── retry_with_more_memory │ ├── preemptible_and_memory_retry.wdl │ ├── retry_with_more_memory.options │ └── retry_with_more_memory.wdl ├── runtime_failOnStderr │ └── runtime_failOnStderr.wdl ├── sizeenginefunction │ └── sizeenginefunction.wdl ├── wdl_optional_outputs_draft2 │ ├── wdl_optional_outputs_draft2.wdl │ └── wdl_optional_outputs_unsupported_draft2.wdl ├── workflow_name_length │ ├── importer.wdl │ ├── importer_ok.wdl │ ├── workflow_name_length.wdl │ └── workflow_name_length_ok.wdl └── workflow_type_and_version_cwl │ └── workflow_type_and_version_cwl.wdl ├── custom_reorg ├── test_reorg.wdl ├── test_reorg_extras.json ├── test_reorg_no_config.wdl └── test_reorg_no_config_extras.json ├── cwl ├── cat.cwl.json ├── cat_input.json ├── cat_results.json ├── tar_files.cwl.json └── tar_files_input.json ├── cwl_conformance ├── generate_tests.py ├── tools │ ├── anon_enum_inside_array.cwl.json │ ├── anon_enum_inside_array_input.json │ ├── anon_enum_inside_array_inside_schemadef.cwl.json │ ├── anon_enum_inside_array_inside_schemadef_input.json │ ├── anon_enum_inside_array_inside_schemadef_results.json │ ├── anon_enum_inside_array_results.json │ ├── bash-dollar-quote.cwl.json │ ├── bash-dollar-quote_results.json │ ├── bash-line-continuation-with-expression.cwl.json │ ├── bash-line-continuation-with-expression_results.json │ ├── bash-line-continuation.cwl.json │ ├── bash-line-continuation_results.json │ ├── bash_line_continuation.cwl.json │ ├── binding-test.cwl.json │ ├── binding-test_input.json │ ├── binding-test_results.json │ ├── bool-empty-inputbinding.cwl.json │ ├── bool-empty-inputbinding_input.json │ ├── bool-empty-inputbinding_results.json │ ├── bwa-mem-tool.cwl.json │ ├── bwa-mem-tool_input.json │ ├── bwa-mem-tool_results.json │ ├── cat-from-dir.cwl.json │ ├── cat-from-dir_input1.json │ ├── cat-from-dir_input2.json │ ├── cat-from-dir_results1.json │ ├── cat-from-dir_results2.json │ ├── cat-tool-shortcut.cwl.json │ ├── cat-tool-shortcut_input.json │ ├── cat-tool-shortcut_results.json │ ├── cat-tool.cwl.json │ ├── cat-tool_input.json │ ├── cat-tool_results.json │ ├── cat1-testcli.cwl.json │ ├── cat1-testcli_input1.json │ ├── cat1-testcli_input2.json │ ├── cat1-testcli_results1.json │ ├── cat1-testcli_results2.json │ ├── cat3-from-dir.cwl.json │ ├── cat3-from-dir_input.json │ ├── cat3-from-dir_results.json │ ├── cat3-nodocker.cwl.json │ ├── cat3-nodocker_input.json │ ├── cat3-nodocker_results.json │ ├── cat3-tool-mediumcut.cwl.json │ ├── cat3-tool-mediumcut_input.json │ ├── cat3-tool-mediumcut_results.json │ ├── cat3-tool-shortcut.cwl.json │ ├── cat3-tool-shortcut_input.json │ ├── cat3-tool-shortcut_results.json │ ├── cat3-tool.cwl.json │ ├── cat3-tool_input1.json │ ├── cat3-tool_input2.json │ ├── cat3-tool_results1.json │ ├── cat3-tool_results2.json │ ├── cat4-tool.cwl.json │ ├── cat4-tool_input.json │ ├── cat4-tool_results.json │ ├── cat5-tool.cwl.json │ ├── cat5-tool_input.json │ ├── cat5-tool_results.json │ ├── cores_float.cwl.json │ ├── cores_float_input.json │ ├── cores_float_results.json │ ├── cwl │ │ ├── hello.txt │ │ ├── literal.txt │ │ └── simple.cwl │ ├── cwloutput-nolimit.cwl.json │ ├── cwloutput-nolimit_results.json │ ├── default_path.cwl.json │ ├── default_path_input.json │ ├── default_path_results.json │ ├── dir.cwl.json │ ├── dir2.cwl.json │ ├── dir2_input.json │ ├── dir2_results.json │ ├── dir3.cwl.json │ ├── dir3_input.json │ ├── dir3_results.json │ ├── dir4.cwl.json │ ├── dir4_input1.json │ ├── dir4_input2.json │ ├── dir4_input3.json │ ├── dir4_results1.json │ ├── dir4_results2.json │ ├── dir4_results3.json │ ├── dir5.cwl.json │ ├── dir5_input.json │ ├── dir5_results.json │ ├── dir6.cwl.json │ ├── dir6_input.json │ ├── dir6_results.json │ ├── dir7.cwl.json │ ├── dir7_input.json │ ├── dir7_results.json │ ├── dir_input.json │ ├── dir_results.json │ ├── docker-array-secondaryfiles.cwl.json │ ├── docker-array-secondaryfiles_input1.json │ ├── docker-array-secondaryfiles_input2.json │ ├── docker-array-secondaryfiles_results1.json │ ├── docker-output-dir.cwl.json │ ├── docker-output-dir_input.json │ ├── docker-output-dir_results.json │ ├── docker-run-cmd.cwl.json │ ├── docker-run-cmd_input.json │ ├── docker-run-cmd_results.json │ ├── dynresreq-dir.cwl.json │ ├── dynresreq-dir_input.json │ ├── dynresreq-dir_results.json │ ├── dynresreq.cwl.json │ ├── dynresreq_input.json │ ├── dynresreq_results.json │ ├── echo-position-expr.cwl.json │ ├── echo-position-expr_input.json │ ├── echo-position-expr_results.json │ ├── echo-tool-packed.cwl.json │ ├── echo-tool-packed2.cwl.json │ ├── echo-tool-packed2_input.json │ ├── echo-tool-packed2_results.json │ ├── echo-tool-packed_input.json │ ├── echo-tool-packed_results.json │ ├── echo-tool.cwl.json │ ├── echo-tool_input1.json │ ├── echo-tool_input2.json │ ├── echo-tool_input3.json │ ├── echo-tool_results1.json │ ├── empty-array-input.cwl.json │ ├── empty-array-input_input.json │ ├── empty-array-input_results.json │ ├── env-tool1.cwl.json │ ├── env-tool1_input.json │ ├── env-tool1_results.json │ ├── env-tool3.cwl.json │ ├── env-tool3_input1.json │ ├── env-tool3_input2.json │ ├── env-tool3_results1.json │ ├── env-tool3_results2.json │ ├── env-tool4.cwl.json │ ├── env-tool4_input.json │ ├── env-tool4_results.json │ ├── envvar.cwl.json │ ├── envvar2.cwl.json │ ├── envvar2_input.json │ ├── envvar2_results.json │ ├── envvar3.cwl.json │ ├── envvar3_input.json │ ├── envvar3_results.json │ ├── envvar_input.json │ ├── envvar_results.json │ ├── exit-success.cwl.json │ ├── exit-success_input.json │ ├── exit-success_results.json │ ├── exitcode.cwl.json │ ├── exitcode_results.json │ ├── file-literal-ex.cwl.json │ ├── file-literal-ex_results.json │ ├── formattest.cwl.json │ ├── formattest2.cwl.json │ ├── formattest2_input.json │ ├── formattest2_results.json │ ├── formattest3.cwl.json │ ├── formattest3_input.json │ ├── formattest3_results.json │ ├── formattest_input.json │ ├── formattest_results.json │ ├── glob-expr-list.cwl.json │ ├── glob-expr-list_input.json │ ├── glob-expr-list_results.json │ ├── glob-path-error.cwl.json │ ├── glob-path-error_input.json │ ├── glob_directory.cwl.json │ ├── glob_directory_input.json │ ├── glob_directory_results.json │ ├── glob_test.cwl.json │ ├── glob_test_input.json │ ├── glob_test_results.json │ ├── imported-hint.cwl.json │ ├── imported-hint_input.json │ ├── imported-hint_results.json │ ├── initialwork-path.cwl.json │ ├── initialwork-path_input.json │ ├── initialwork-path_results.json │ ├── initialworkdir-glob-fullpath.cwl.json │ ├── initialworkdir-glob-fullpath_input1.json │ ├── initialworkdir-glob-fullpath_input2.json │ ├── initialworkdir-glob-fullpath_results1.json │ ├── initialworkdir-glob-fullpath_results2.json │ ├── initialworkdirrequirement-docker-out.cwl.json │ ├── initialworkdirrequirement-docker-out_input.json │ ├── initialworkdirrequirement-docker-out_results.json │ ├── inline-js.cwl.json │ ├── inline-js_input.json │ ├── inline-js_results.json │ ├── io-file-or-files.cwl.json │ ├── io-file-or-files_input1.json │ ├── io-file-or-files_input2.json │ ├── io-file-or-files_input3.json │ ├── io-file-or-files_input4.json │ ├── io-file-or-files_results1.json │ ├── io-file-or-files_results2.json │ ├── io-file-or-files_results3.json │ ├── io-file-or-files_results4.json │ ├── iwd-container-entryname1.cwl.json │ ├── iwd-container-entryname1_input.json │ ├── iwd-container-entryname1_results.json │ ├── iwd-container-entryname2.cwl.json │ ├── iwd-container-entryname2_input.json │ ├── iwd-container-entryname3.cwl.json │ ├── iwd-container-entryname3_input.json │ ├── iwd-container-entryname4.cwl.json │ ├── iwd-container-entryname4_input.json │ ├── iwd-fileobjs.cwl.json │ ├── iwd-fileobjs1.cwl.json │ ├── iwd-fileobjs1_results.json │ ├── iwd-fileobjs2.cwl.json │ ├── iwd-fileobjs2_results.json │ ├── iwd-fileobjs_results.json │ ├── iwd-jsondump1-nl.cwl.json │ ├── iwd-jsondump1-nl_results.json │ ├── iwd-jsondump1.cwl.json │ ├── iwd-jsondump1_results.json │ ├── iwd-jsondump2-nl.cwl.json │ ├── iwd-jsondump2-nl_results.json │ ├── iwd-jsondump2.cwl.json │ ├── iwd-jsondump2_results.json │ ├── iwd-jsondump3-nl.cwl.json │ ├── iwd-jsondump3-nl_results.json │ ├── iwd-jsondump3.cwl.json │ ├── iwd-jsondump3_results.json │ ├── iwd-nolimit.cwl.json │ ├── iwd-nolimit_results.json │ ├── iwd-passthrough1.cwl.json │ ├── iwd-passthrough1_input.json │ ├── iwd-passthrough1_results.json │ ├── iwd-passthrough2.cwl.json │ ├── iwd-passthrough2_input.json │ ├── iwd-passthrough2_results.json │ ├── iwd-passthrough3.cwl.json │ ├── iwd-passthrough3_input.json │ ├── iwd-passthrough3_results.json │ ├── iwd-passthrough4.cwl.json │ ├── iwd-passthrough4_input.json │ ├── iwd-passthrough4_results.json │ ├── iwdr-entry.cwl.json │ ├── iwdr-entry_input.json │ ├── iwdr-entry_results.json │ ├── iwdr_dir_literal_real_file.cwl.json │ ├── iwdr_dir_literal_real_file_input.json │ ├── iwdr_dir_literal_real_file_results.json │ ├── js-quote.cwl.json │ ├── js-quote_results.json │ ├── linkfile.cwl.json │ ├── linkfile_input.json │ ├── linkfile_results.json │ ├── listing_deep1.cwl.json │ ├── listing_deep1_input.json │ ├── listing_deep1_results.json │ ├── listing_deep2.cwl.json │ ├── listing_deep2_input.json │ ├── listing_deep2_results.json │ ├── listing_none1.cwl.json │ ├── listing_none1_input.json │ ├── listing_none1_results.json │ ├── listing_none2.cwl.json │ ├── listing_none2_input.json │ ├── listing_none2_results.json │ ├── listing_none3.cwl.json │ ├── listing_none3_input.json │ ├── listing_none3_results.json │ ├── listing_shallow1.cwl.json │ ├── listing_shallow1_input.json │ ├── listing_shallow1_results.json │ ├── listing_shallow2.cwl.json │ ├── listing_shallow2_input.json │ ├── listing_shallow2_results.json │ ├── loadContents-limit.cwl.json │ ├── loadContents-limit_input.json │ ├── loadContents-limit_results.json │ ├── metadata.cwl.json │ ├── metadata_input.json │ ├── metadata_results.json │ ├── nameroot.cwl.json │ ├── nameroot_input.json │ ├── nameroot_results.json │ ├── nested-array.cwl.json │ ├── nested-array_input.json │ ├── nested-array_results.json │ ├── networkaccess.cwl.json │ ├── networkaccess2.cwl.json │ ├── networkaccess2_input.json │ ├── networkaccess_input.json │ ├── networkaccess_results.json │ ├── no-inputs-tool.cwl.json │ ├── no-inputs-tool_results.json │ ├── no-outputs-tool.cwl.json │ ├── no-outputs-tool_input.json │ ├── no-outputs-tool_results.json │ ├── null-defined.cwl.json │ ├── null-defined_input1.json │ ├── null-defined_input2.json │ ├── null-defined_results1.json │ ├── null-defined_results2.json │ ├── null-expression1-tool.cwl.json │ ├── null-expression2-tool.cwl.json │ ├── null-expression2-tool_input1.json │ ├── null-expression2-tool_input2.json │ ├── null-expression2-tool_input3.json │ ├── null-expression2-tool_results3.json │ ├── optional-numerical-output-0.cwl.json │ ├── optional-numerical-output-0_results.json │ ├── optional-output.cwl.json │ ├── optional-output_input.json │ ├── optional-output_results.json │ ├── output-arrays-int.cwl.json │ ├── output-arrays-int_input.json │ ├── output-arrays-int_results.json │ ├── params.cwl.json │ ├── params2.cwl.json │ ├── params2_input.json │ ├── params2_results.json │ ├── params_input.json │ ├── params_results.json │ ├── parseInt-tool.cwl.json │ ├── parseInt-tool_input.json │ ├── parseInt-tool_results.json │ ├── record-in-format.cwl.json │ ├── record-in-format_input1.json │ ├── record-in-format_input2.json │ ├── record-in-format_input3.json │ ├── record-in-format_input4.json │ ├── record-in-secondaryFiles.cwl.json │ ├── record-in-secondaryFiles_input.json │ ├── record-in-secondaryFiles_results.json │ ├── record-out-format.cwl.json │ ├── record-out-format_input.json │ ├── record-out-format_results.json │ ├── record-out-secondaryFiles.cwl.json │ ├── record-out-secondaryFiles_input.json │ ├── record-out-secondaryFiles_results.json │ ├── record-output.cwl.json │ ├── record-output_input.json │ ├── record-output_results.json │ ├── record-sd-secondaryFiles.cwl.json │ ├── record-sd-secondaryFiles_input.json │ ├── record-sd-secondaryFiles_results.json │ ├── recursive-input-directory.cwl.json │ ├── recursive-input-directory_input.json │ ├── recursive-input-directory_results.json │ ├── rename-inputs.cwl.json │ ├── rename-inputs_input.json │ ├── rename-inputs_results.json │ ├── rename-outputs.cwl.json │ ├── rename-outputs_results.json │ ├── rename.cwl.json │ ├── rename_input.json │ ├── rename_results.json │ ├── runtime-paths-distinct.cwl.json │ ├── runtime-paths-distinct_input.json │ ├── runtime-paths-distinct_results.json │ ├── schemadef-tool.cwl.json │ ├── schemadef-tool_input.json │ ├── schemadef-tool_results.json │ ├── shellchar.cwl.json │ ├── shellchar2.cwl.json │ ├── shellchar2_input.json │ ├── shellchar2_results.json │ ├── shellchar_input.json │ ├── shellchar_results.json │ ├── size-expression-tool.cwl.json │ ├── size-expression-tool_input1.json │ ├── size-expression-tool_input2.json │ ├── size-expression-tool_results1.json │ ├── size-expression-tool_results2.json │ ├── stage-array-dirs.cwl.json │ ├── stage-array-dirs_input.json │ ├── stage-array-dirs_results.json │ ├── stage-array.cwl.json │ ├── stage-array_input.json │ ├── stage-array_results.json │ ├── stage-unprovided-file.cwl.json │ ├── stage-unprovided-file_input.json │ ├── stage-unprovided-file_results.json │ ├── stage_file_array.cwl.json │ ├── stage_file_array_basename.cwl.json │ ├── stage_file_array_basename_and_entryname.cwl.json │ ├── stage_file_array_basename_and_entryname_input.json │ ├── stage_file_array_basename_and_entryname_results.json │ ├── stage_file_array_basename_input.json │ ├── stage_file_array_basename_results.json │ ├── stage_file_array_input.json │ ├── stage_file_array_results.json │ ├── stagefile.cwl.json │ ├── stagefile_input.json │ ├── stagefile_results.json │ ├── stderr-mediumcut.cwl.json │ ├── stderr-mediumcut_input.json │ ├── stderr-mediumcut_results.json │ ├── stderr-shortcut.cwl.json │ ├── stderr-shortcut_input.json │ ├── stderr-shortcut_results.json │ ├── stderr.cwl.json │ ├── stderr_input.json │ ├── stderr_results.json │ ├── storage_float.cwl.json │ ├── storage_float_input.json │ ├── storage_float_results.json │ ├── symlink-illegal.cwl.json │ ├── symlink-illegal_input.json │ ├── symlink-illegal_results.json │ ├── symlink-legal.cwl.json │ ├── symlink-legal_input.json │ ├── symlink-legal_results.json │ ├── template-tool.cwl.json │ ├── template-tool_input.json │ ├── template-tool_results.json │ ├── test-cwl-out.cwl.json │ ├── test-cwl-out2.cwl.json │ ├── test-cwl-out2_input.json │ ├── test-cwl-out2_results.json │ ├── test-cwl-out_input.json │ ├── test-cwl-out_results.json │ ├── test │ │ └── special_file │ ├── timelimit.cwl.json │ ├── timelimit2.cwl.json │ ├── timelimit2_input.json │ ├── timelimit3.cwl.json │ ├── timelimit3_input.json │ ├── timelimit3_results.json │ ├── timelimit4.cwl.json │ ├── timelimit4_input.json │ ├── timelimit5.cwl.json │ ├── timelimit5_results.json │ ├── timelimit_input.json │ ├── tmap-tool.cwl.json │ ├── tmap-tool_input.json │ ├── tmap-tool_results.json │ ├── valueFrom-constant.cwl.json │ ├── valueFrom-constant_input.json │ ├── valueFrom-constant_results.json │ ├── vf-concat.cwl.json │ ├── vf-concat_input1.json │ ├── vf-concat_input2.json │ ├── vf-concat_results1.json │ ├── vf-concat_results2.json │ ├── wc2-tool.cwl.json │ ├── wc2-tool_input.json │ ├── wc2-tool_results.json │ ├── wc4-tool.cwl.json │ ├── wc4-tool_input.json │ ├── wc4-tool_results.json │ ├── writable-dir-docker.cwl.json │ ├── writable-dir-docker_input.json │ ├── writable-dir-docker_results.json │ ├── writable-dir.cwl.json │ ├── writable-dir_input.json │ └── writable-dir_results.json └── workflows │ ├── any-type-compat.cwl.json │ ├── any-type-compat_input.json │ ├── any-type-compat_results.json │ ├── basename-fields-test.cwl.json │ ├── basename-fields-test_input.json │ ├── basename-fields-test_results.json │ ├── cond-wf-001.cwl.json │ ├── cond-wf-001_input1.json │ ├── cond-wf-001_input2.json │ ├── cond-wf-001_nojs.cwl.json │ ├── cond-wf-001_nojs_input1.json │ ├── cond-wf-001_nojs_input2.json │ ├── cond-wf-001_nojs_results1.json │ ├── cond-wf-001_nojs_results2.json │ ├── cond-wf-001_results1.json │ ├── cond-wf-001_results2.json │ ├── cond-wf-002.cwl.json │ ├── cond-wf-002_input.json │ ├── cond-wf-002_nojs.cwl.json │ ├── cond-wf-002_nojs_input.json │ ├── cond-wf-002_nojs_results.json │ ├── cond-wf-002_results.json │ ├── cond-wf-003-1.cwl.json │ ├── cond-wf-003-1_input1.json │ ├── cond-wf-003-1_input2.json │ ├── cond-wf-003-1_input3.json │ ├── cond-wf-003-1_nojs.cwl.json │ ├── cond-wf-003-1_nojs_input1.json │ ├── cond-wf-003-1_nojs_input2.json │ ├── cond-wf-003-1_nojs_input3.json │ ├── cond-wf-003-1_nojs_results1.json │ ├── cond-wf-003-1_nojs_results3.json │ ├── cond-wf-003-1_results1.json │ ├── cond-wf-003-1_results2.json │ ├── cond-wf-003-1_results3.json │ ├── cond-wf-003.cwl.json │ ├── cond-wf-003_input1.json │ ├── cond-wf-003_input2.json │ ├── cond-wf-003_nojs.cwl.json │ ├── cond-wf-003_nojs_input1.json │ ├── cond-wf-003_nojs_input2.json │ ├── cond-wf-003_nojs_results1.json │ ├── cond-wf-003_nojs_results2.json │ ├── cond-wf-003_results1.json │ ├── cond-wf-003_results2.json │ ├── cond-wf-004.cwl.json │ ├── cond-wf-004_input1.json │ ├── cond-wf-004_input2.json │ ├── cond-wf-004_nojs.cwl.json │ ├── cond-wf-004_nojs_input1.json │ ├── cond-wf-004_nojs_input2.json │ ├── cond-wf-004_nojs_results1.json │ ├── cond-wf-004_results1.json │ ├── cond-wf-005.cwl.json │ ├── cond-wf-005_input.json │ ├── cond-wf-005_nojs.cwl.json │ ├── cond-wf-005_nojs_input.json │ ├── cond-wf-006.cwl.json │ ├── cond-wf-006_input1.json │ ├── cond-wf-006_input2.json │ ├── cond-wf-006_nojs.cwl.json │ ├── cond-wf-006_nojs_input1.json │ ├── cond-wf-006_nojs_input2.json │ ├── cond-wf-006_nojs_results1.json │ ├── cond-wf-006_results1.json │ ├── cond-wf-007.cwl.json │ ├── cond-wf-007_input1.json │ ├── cond-wf-007_input2.json │ ├── cond-wf-007_input3.json │ ├── cond-wf-007_nojs.cwl.json │ ├── cond-wf-007_nojs_input1.json │ ├── cond-wf-007_nojs_input2.json │ ├── cond-wf-007_nojs_input3.json │ ├── cond-wf-007_nojs_results1.json │ ├── cond-wf-007_nojs_results2.json │ ├── cond-wf-007_nojs_results3.json │ ├── cond-wf-007_results1.json │ ├── cond-wf-007_results2.json │ ├── cond-wf-007_results3.json │ ├── cond-wf-009.cwl.json │ ├── cond-wf-009_input1.json │ ├── cond-wf-009_input2.json │ ├── cond-wf-009_nojs.cwl.json │ ├── cond-wf-009_nojs_input1.json │ ├── cond-wf-009_nojs_input2.json │ ├── cond-wf-009_nojs_results1.json │ ├── cond-wf-009_nojs_results2.json │ ├── cond-wf-009_results1.json │ ├── cond-wf-009_results2.json │ ├── cond-wf-010.cwl.json │ ├── cond-wf-010_input.json │ ├── cond-wf-010_nojs.cwl.json │ ├── cond-wf-010_nojs_input.json │ ├── cond-wf-010_nojs_results.json │ ├── cond-wf-010_results.json │ ├── cond-wf-011.cwl.json │ ├── cond-wf-011_input.json │ ├── cond-wf-011_nojs.cwl.json │ ├── cond-wf-011_nojs_input.json │ ├── cond-wf-011_nojs_results.json │ ├── cond-wf-011_results.json │ ├── cond-wf-012.cwl.json │ ├── cond-wf-012_input.json │ ├── cond-wf-012_nojs.cwl.json │ ├── cond-wf-012_nojs_input.json │ ├── cond-wf-013.cwl.json │ ├── cond-wf-013_input.json │ ├── cond-wf-013_nojs.cwl.json │ ├── cond-wf-013_nojs_input.json │ ├── cond-wf-013_nojs_results.json │ ├── cond-wf-013_results.json │ ├── cond-with-defaults.cwl.json │ ├── cond-with-defaults_input1.json │ ├── cond-with-defaults_input2.json │ ├── cond-with-defaults_results1.json │ ├── cond-with-defaults_results2.json │ ├── conflict-wf.cwl.json │ ├── conflict-wf_input.json │ ├── conflict-wf_results.json │ ├── count-lines1-wf.cwl.json │ ├── count-lines1-wf_input.json │ ├── count-lines1-wf_results.json │ ├── count-lines10-wf.cwl.json │ ├── count-lines10-wf_input.json │ ├── count-lines10-wf_results.json │ ├── count-lines11-extra-step-wf-noET.cwl.json │ ├── count-lines11-extra-step-wf-noET_input.json │ ├── count-lines11-extra-step-wf-noET_results.json │ ├── count-lines11-extra-step-wf.cwl.json │ ├── count-lines11-extra-step-wf_input.json │ ├── count-lines11-extra-step-wf_results.json │ ├── count-lines11-null-step-wf-noET.cwl.json │ ├── count-lines11-null-step-wf-noET_input.json │ ├── count-lines11-null-step-wf-noET_results.json │ ├── count-lines11-null-step-wf.cwl.json │ ├── count-lines11-null-step-wf_input.json │ ├── count-lines11-null-step-wf_results.json │ ├── count-lines11-wf-noET.cwl.json │ ├── count-lines11-wf-noET_input.json │ ├── count-lines11-wf-noET_results.json │ ├── count-lines11-wf.cwl.json │ ├── count-lines11-wf_input1.json │ ├── count-lines11-wf_input2.json │ ├── count-lines11-wf_input3.json │ ├── count-lines11-wf_results1.json │ ├── count-lines11-wf_results2.json │ ├── count-lines11-wf_results3.json │ ├── count-lines12-wf.cwl.json │ ├── count-lines12-wf_input.json │ ├── count-lines12-wf_results.json │ ├── count-lines13-wf.cwl.json │ ├── count-lines13-wf_input.json │ ├── count-lines13-wf_results.json │ ├── count-lines14-wf.cwl.json │ ├── count-lines14-wf_input.json │ ├── count-lines14-wf_results.json │ ├── count-lines15-wf.cwl.json │ ├── count-lines15-wf_input.json │ ├── count-lines15-wf_results.json │ ├── count-lines16-wf.cwl.json │ ├── count-lines16-wf_input.json │ ├── count-lines16-wf_results.json │ ├── count-lines17-wf.cwl.json │ ├── count-lines17-wf_input.json │ ├── count-lines17-wf_results.json │ ├── count-lines18-wf.cwl.json │ ├── count-lines18-wf_input.json │ ├── count-lines18-wf_results.json │ ├── count-lines19-wf.cwl.json │ ├── count-lines19-wf_input.json │ ├── count-lines19-wf_results.json │ ├── count-lines2-wf.cwl.json │ ├── count-lines2-wf_input.json │ ├── count-lines2-wf_results.json │ ├── count-lines3-wf.cwl.json │ ├── count-lines3-wf_input.json │ ├── count-lines3-wf_results.json │ ├── count-lines4-wf.cwl.json │ ├── count-lines4-wf_input.json │ ├── count-lines4-wf_results.json │ ├── count-lines5-wf.cwl.json │ ├── count-lines5-wf_input1.json │ ├── count-lines5-wf_input2.json │ ├── count-lines5-wf_results1.json │ ├── count-lines5-wf_results2.json │ ├── count-lines6-wf.cwl.json │ ├── count-lines6-wf_input.json │ ├── count-lines6-wf_results.json │ ├── count-lines7-wf.cwl.json │ ├── count-lines7-wf_input.json │ ├── count-lines7-wf_results.json │ ├── count-lines8-wf-noET.cwl.json │ ├── count-lines8-wf-noET_input.json │ ├── count-lines8-wf-noET_results.json │ ├── count-lines8-wf.cwl.json │ ├── count-lines8-wf_input.json │ ├── count-lines8-wf_results.json │ ├── count-lines9-wf-noET.cwl.json │ ├── count-lines9-wf-noET_input.json │ ├── count-lines9-wf-noET_results.json │ ├── count-lines9-wf.cwl.json │ ├── count-lines9-wf_input.json │ ├── count-lines9-wf_results.json │ ├── dynresreq-workflow-inputdefault.cwl.json │ ├── dynresreq-workflow-inputdefault_input.json │ ├── dynresreq-workflow-inputdefault_results.json │ ├── dynresreq-workflow-stepdefault.cwl.json │ ├── dynresreq-workflow-stepdefault_input.json │ ├── dynresreq-workflow-stepdefault_results.json │ ├── dynresreq-workflow-tooldefault.cwl.json │ ├── dynresreq-workflow-tooldefault_input.json │ ├── dynresreq-workflow-tooldefault_results.json │ ├── dynresreq-workflow.cwl.json │ ├── dynresreq-workflow_input.json │ ├── dynresreq-workflow_results.json │ ├── dynresreq_input.json │ ├── dynresreq_results.json │ ├── echo-wf-default.cwl.json │ ├── echo-wf-default_input.json │ ├── echo-wf-default_results.json │ ├── env-wf1.cwl.json │ ├── env-wf1_input.json │ ├── env-wf1_results.json │ ├── env-wf2.cwl.json │ ├── env-wf2_input.json │ ├── env-wf2_results.json │ ├── env-wf3.cwl.json │ ├── env-wf3_input.json │ ├── env-wf3_results.json │ ├── fail-unconnected.cwl.json │ ├── fail-unconnected_input.json │ ├── import_schema-def_packed.cwl.json │ ├── import_schema-def_packed_input.json │ ├── import_schema-def_packed_results.json │ ├── inp_update_wf.cwl.json │ ├── inpdir_update_wf.cwl.json │ ├── inpdir_update_wf_results.json │ ├── io-any-wf-1.cwl.json │ ├── io-any-wf-1_input1.json │ ├── io-any-wf-1_input2.json │ ├── io-any-wf-1_input3.json │ ├── io-any-wf-1_input4.json │ ├── io-any-wf-1_input5.json │ ├── io-any-wf-1_results1.json │ ├── io-any-wf-1_results2.json │ ├── io-any-wf-1_results3.json │ ├── io-any-wf-1_results4.json │ ├── io-any-wf-1_results5.json │ ├── io-file-default-wf.cwl.json │ ├── io-file-default-wf_input1.json │ ├── io-file-default-wf_input2.json │ ├── io-file-default-wf_results1.json │ ├── io-file-default-wf_results2.json │ ├── io-int-default-tool-and-wf.cwl.json │ ├── io-int-default-tool-and-wf_input.json │ ├── io-int-default-tool-and-wf_results.json │ ├── io-int-default-wf.cwl.json │ ├── io-int-default-wf_input1.json │ ├── io-int-default-wf_input2.json │ ├── io-int-default-wf_results1.json │ ├── io-int-default-wf_results2.json │ ├── io-int-optional-wf.cwl.json │ ├── io-int-optional-wf_input1.json │ ├── io-int-optional-wf_input2.json │ ├── io-int-optional-wf_results1.json │ ├── io-int-optional-wf_results2.json │ ├── io-int-wf.cwl.json │ ├── io-int-wf_input.json │ ├── io-int-wf_results.json │ ├── io-union-input-default-wf.cwl.json │ ├── io-union-input-default-wf_input1.json │ ├── io-union-input-default-wf_input2.json │ ├── io-union-input-default-wf_results1.json │ ├── io-union-input-default-wf_results2.json │ ├── iwdr_with_nested_dirs.cwl.json │ ├── iwdr_with_nested_dirs_results.json │ ├── js-expr-req-wf.cwl.json │ ├── js-expr-req-wf_results.json │ ├── no-inputs-wf.cwl.json │ ├── no-inputs-wf_results.json │ ├── no-outputs-wf.cwl.json │ ├── no-outputs-wf_input.json │ ├── no-outputs-wf_results.json │ ├── output-arrays-file-wf.cwl.json │ ├── output-arrays-file-wf_input.json │ ├── output-arrays-file-wf_results.json │ ├── output-arrays-int-wf.cwl.json │ ├── output-arrays-int-wf_input.json │ ├── output-arrays-int-wf_results.json │ ├── parseInt-tool_input.json │ ├── parseInt-tool_results.json │ ├── pass-unconnected.cwl.json │ ├── pass-unconnected_input.json │ ├── pass-unconnected_results.json │ ├── record-in-secondaryFiles-missing-wf.cwl.json │ ├── record-in-secondaryFiles-missing-wf_input.json │ ├── record-in-secondaryFiles-wf.cwl.json │ ├── record-in-secondaryFiles-wf_input.json │ ├── record-output-wf.cwl.json │ ├── record-output-wf_input.json │ ├── record-output-wf_results.json │ ├── record-output_input.json │ ├── record-output_results.json │ ├── revsort-packed.cwl.json │ ├── revsort-packed_input.json │ ├── revsort-packed_results.json │ ├── revsort.cwl.json │ ├── revsort_input.json │ ├── revsort_results.json │ ├── scatter-valuefrom-inputs-wf1.cwl.json │ ├── scatter-valuefrom-inputs-wf1_input.json │ ├── scatter-valuefrom-inputs-wf1_results.json │ ├── scatter-valuefrom-wf1.cwl.json │ ├── scatter-valuefrom-wf1_input.json │ ├── scatter-valuefrom-wf1_results.json │ ├── scatter-valuefrom-wf2.cwl.json │ ├── scatter-valuefrom-wf2_input.json │ ├── scatter-valuefrom-wf2_results.json │ ├── scatter-valuefrom-wf3.cwl.json │ ├── scatter-valuefrom-wf3_input.json │ ├── scatter-valuefrom-wf3_results.json │ ├── scatter-valuefrom-wf4.cwl.json │ ├── scatter-valuefrom-wf4_input.json │ ├── scatter-valuefrom-wf4_results.json │ ├── scatter-valuefrom-wf5.cwl.json │ ├── scatter-valuefrom-wf5_input.json │ ├── scatter-valuefrom-wf5_results.json │ ├── scatter-valuefrom-wf6.cwl.json │ ├── scatter-valuefrom-wf6_input.json │ ├── scatter-valuefrom-wf6_results.json │ ├── scatter-wf1.cwl.json │ ├── scatter-wf1_input.json │ ├── scatter-wf1_results.json │ ├── scatter-wf2.cwl.json │ ├── scatter-wf2_input1.json │ ├── scatter-wf2_input2.json │ ├── scatter-wf2_results1.json │ ├── scatter-wf2_results2.json │ ├── scatter-wf3.cwl.json │ ├── scatter-wf3_input1.json │ ├── scatter-wf3_input2.json │ ├── scatter-wf3_input3.json │ ├── scatter-wf3_results1.json │ ├── scatter-wf3_results2.json │ ├── scatter-wf3_results3.json │ ├── scatter-wf4.cwl.json │ ├── scatter-wf4_input1.json │ ├── scatter-wf4_input2.json │ ├── scatter-wf4_results1.json │ ├── scatter-wf4_results2.json │ ├── schemadef-tool_input.json │ ├── schemadef-tool_results.json │ ├── schemadef-wf.cwl.json │ ├── schemadef-wf_input.json │ ├── schemadef-wf_results.json │ ├── search.cwl.json │ ├── search_input.json │ ├── search_results.json │ ├── step-valuefrom-wf.cwl.json │ ├── step-valuefrom-wf_input.json │ ├── step-valuefrom-wf_results.json │ ├── step-valuefrom2-wf.cwl.json │ ├── step-valuefrom2-wf_input.json │ ├── step-valuefrom2-wf_results.json │ ├── step-valuefrom3-wf.cwl.json │ ├── step-valuefrom3-wf_input.json │ ├── step-valuefrom3-wf_results.json │ ├── step-valuefrom4-wf.cwl.json │ ├── step-valuefrom4-wf_input.json │ ├── step-valuefrom4-wf_results.json │ ├── step-valuefrom5-wf.cwl.json │ ├── step-valuefrom5-wf_input.json │ ├── step-valuefrom5-wf_results.json │ ├── steplevel-resreq.cwl.json │ ├── steplevel-resreq_input.json │ ├── steplevel-resreq_results.json │ ├── sum-wf-noET.cwl.json │ ├── sum-wf-noET_input.json │ ├── sum-wf-noET_results.json │ ├── sum-wf.cwl.json │ ├── sum-wf_input.json │ ├── sum-wf_results.json │ ├── timelimit-wf.cwl.json │ ├── timelimit-wf_input.json │ ├── timelimit2-wf.cwl.json │ ├── timelimit2-wf_input.json │ ├── timelimit2-wf_results.json │ ├── timelimit3-wf.cwl.json │ ├── timelimit3-wf_input.json │ ├── timelimit3-wf_results.json │ ├── timelimit4-wf.cwl.json │ ├── timelimit4-wf_input.json │ ├── wc2-tool_input.json │ ├── wc2-tool_results.json │ ├── wf-loadContents.cwl.json │ ├── wf-loadContents2.cwl.json │ ├── wf-loadContents2_input.json │ ├── wf-loadContents2_results.json │ ├── wf-loadContents3.cwl.json │ ├── wf-loadContents3_input.json │ ├── wf-loadContents3_results.json │ ├── wf-loadContents4.cwl.json │ ├── wf-loadContents4_input.json │ ├── wf-loadContents4_results.json │ ├── wf-loadContents_input.json │ └── wf-loadContents_results.json ├── cwl_cromwell ├── InitialWorkDirRequirement │ ├── file_array_listing.cwl │ ├── file_array_listing.cwl.json │ ├── file_array_listing_input.yaml │ ├── inline_file.cwl │ ├── inline_file.cwl.json │ ├── inline_file_custom_entryname.cwl │ ├── inline_file_custom_entryname.cwl.json │ ├── inline_file_custom_entryname_input.yaml │ ├── inline_file_input.yaml │ ├── input_string.cwl │ ├── input_string.cwl.json │ ├── input_string_function.cwl │ ├── input_string_function.cwl.json │ ├── input_string_function_input.yaml │ └── input_string_input.yaml ├── cwl_ad_hoc_file_test │ ├── cwl-test.cwl │ ├── cwl-test.cwl.json │ ├── cwl-test_input.yaml │ ├── cwl_ad_hoc_file_test.cwl │ ├── cwl_ad_hoc_file_test.cwl.json │ └── cwl_ad_hoc_file_test_input.json ├── cwl_cache_between_workflows │ ├── cwl_cache_between_workflows.cwl │ ├── cwl_cache_between_workflows.cwl.json │ └── cwl_cache_between_workflows_input.yaml ├── cwl_cache_within_workflow │ ├── cwl_cache_within_workflow.cwl │ ├── cwl_cache_within_workflow.cwl.json │ └── cwl_cache_within_workflow_input.yaml ├── cwl_docker_size │ ├── cwl_docker_size.cwl │ ├── cwl_docker_size.cwl.json │ ├── cwl_docker_size_input.txt │ └── cwl_docker_size_input.yaml ├── cwl_dynamic_initial_workdir │ ├── cwl_dynamic_initial_workdir.cwl │ ├── cwl_dynamic_initial_workdir.cwl.json │ └── cwl_dynamic_initial_workdir_input.yaml ├── cwl_expressionLib │ ├── cwl_expressionLib.cwl │ ├── cwl_expressionLib.cwl.json │ └── cwl_expressionLib_input.yaml ├── cwl_format │ ├── cwl_format.cwl │ ├── cwl_format.cwl.json │ ├── cwl_format_input.yaml │ ├── cwl_format_invalid.yaml │ ├── cwl_format_missing.yaml │ ├── cwl_format_url.cwl │ ├── cwl_format_url.cwl.json │ ├── cwl_format_url_input.yaml │ ├── cwl_format_valid.yaml │ ├── foo.fasta │ └── foo.fastq ├── cwl_glob_sort │ ├── cwl_glob_sort.cwl │ ├── cwl_glob_sort.cwl.json │ └── cwl_glob_sort_input.yaml ├── cwl_hello │ ├── cwl_hello.cwl │ ├── cwl_hello.cwl.json │ └── cwl_hello_input.yaml ├── cwl_http_inputs │ ├── cwl_http_inputs.cwl │ ├── cwl_http_inputs.cwl.json │ └── cwl_http_inputs_input.yaml ├── cwl_import_type │ ├── capture_kit.yml │ ├── test_wf.cwl │ ├── test_wf.cwl.json │ ├── test_wf_input.json │ ├── test_wf_input_ignored.yaml │ ├── touch.cwl │ ├── touch.cwl.json │ └── touch_input.yaml ├── cwl_import_type_packed │ ├── capture_kit.yml │ ├── test_pack.cwl │ ├── test_pack.cwl.json │ ├── test_pack_input.json │ └── test_pack_input_ignore.yaml ├── cwl_input_binding_expression │ ├── cwl_input_binding_expression.cwl │ ├── cwl_input_binding_expression.cwl.json │ └── cwl_input_binding_expression_input.yaml ├── cwl_input_json │ ├── cwl_input_json.cwl │ ├── cwl_input_json.cwl.json │ └── cwl_input_json_input.yaml ├── cwl_input_typearray │ ├── cwl_input_typearray.cwl │ ├── cwl_input_typearray.cwl.json │ └── cwl_input_typearray_input.yaml ├── cwl_interpolated_strings │ ├── cwl_interpolated_strings.cwl │ ├── cwl_interpolated_strings.cwl.json │ └── cwl_interpolated_strings_input.yaml ├── cwl_optionals │ ├── cwl_optionals.cwl │ ├── cwl_optionals.cwl.json │ ├── cwl_optionals.json │ └── cwl_optionals_input.yaml ├── cwl_output_json │ ├── cwl_output_json.cwl │ ├── cwl_output_json.cwl.json │ └── cwl_output_json_input.yaml ├── cwl_prefix_for_array │ ├── prefix_for_array.cwl │ ├── prefix_for_array.cwl.json │ └── prefix_for_array_input.yaml ├── cwl_recursive_link_directories │ ├── cwl_recursive_link_directories.cwl │ ├── cwl_recursive_link_directories.cwl.json │ └── cwl_recursive_link_directories_input.yaml ├── cwl_relative_imports │ ├── cwl_relative_imports.cwl │ ├── cwl_relative_imports.cwl.json │ ├── cwl_relative_imports_glob_sort.cwl │ └── cwl_relative_imports_glob_sort.cwl.json ├── cwl_resources │ ├── cwl_disk_resources.cwl │ ├── cwl_disk_resources.cwl.json │ ├── cwl_disk_resources_input.yaml │ ├── cwl_inputdir_zero_doesnt_localize.cwl │ ├── cwl_inputdir_zero_doesnt_localize.cwl.json │ ├── cwl_inputdir_zero_doesnt_localize_input.yaml │ ├── cwl_resources.cwl │ ├── cwl_resources.cwl.json │ └── cwl_resources_input.yaml ├── cwl_restart │ ├── cwl_restart.cwl │ ├── cwl_restart.cwl.json │ └── cwl_restart_input.yaml ├── cwl_run │ ├── 1st-tool.cwl │ ├── 1st-tool.cwl.json │ └── 1st-tool_input.yaml ├── cwl_secondary_files │ ├── bam.txt │ ├── bam.txt.also │ ├── bar.txt │ ├── bar.txt.also │ ├── baz.txt │ ├── baz.txt.also │ ├── bim.txt │ ├── bim.txt.also │ ├── cwl_secondary_files.cwl │ ├── cwl_secondary_files.cwl.json │ ├── cwl_secondary_files_input.yaml │ ├── foo.txt │ └── foo.txt.also ├── cwl_secondary_files_workflow │ ├── cwl_secondary_files_workflow.cwl │ ├── cwl_secondary_files_workflow.cwl.json │ └── cwl_secondary_files_workflow_input.yaml ├── cwl_stdout_expression │ ├── cwl_stdout_expression.cwl │ ├── cwl_stdout_expression.cwl.json │ └── cwl_stdout_expression_input.yaml ├── cwl_three_step │ ├── cwl_three_step.cwl │ ├── cwl_three_step.cwl.json │ ├── cwl_three_step_caller_wf.cwl │ ├── cwl_three_step_caller_wf.cwl.json │ ├── cwl_three_step_caller_wf_input.yaml │ └── cwl_three_step_input.yaml └── cwls │ ├── cwl_scatter-wf1.cwl │ ├── cwl_scatter-wf1.cwl.json │ └── cwl_scatter-wf1_input.yaml ├── cwl_selected_wf ├── analysis-workflows │ └── definitions │ │ ├── pipelines │ │ ├── alignment_exome.cwl │ │ ├── detect_variants.cwl │ │ ├── germline_exome.cwl │ │ ├── germline_exome_hla_typing.cwl │ │ ├── immuno.cwl │ │ ├── immuno.cwl.json │ │ ├── immuno_input.yaml │ │ ├── labelled_file.yml │ │ ├── rnaseq.cwl │ │ ├── sequence_data.yml │ │ ├── somatic_exome.cwl │ │ ├── trimming_options.yml │ │ └── vep_custom_annotation.yml │ │ ├── subworkflows │ │ ├── bam_readcount.cwl │ │ ├── bam_to_trimmed_fastq_and_hisat_alignments.cwl │ │ ├── bgzip_and_index.cwl │ │ ├── docm_cle.cwl │ │ ├── filter_vcf.cwl │ │ ├── fp_filter.cwl │ │ ├── gatk_haplotypecaller_iterator.cwl │ │ ├── germline_detect_variants.cwl │ │ ├── germline_filter_vcf.cwl │ │ ├── hs_metrics.cwl │ │ ├── labelled_file.yml │ │ ├── mutect.cwl │ │ ├── normalize_variants.cwl │ │ ├── phase_vcf.cwl │ │ ├── pindel.cwl │ │ ├── pindel_cat.cwl │ │ ├── pvacseq.cwl │ │ ├── qc_exome.cwl │ │ ├── sequence_align_and_tag_adapter.cwl │ │ ├── sequence_data.yml │ │ ├── sequence_to_bqsr.cwl │ │ ├── strelka_and_post_processing.cwl │ │ ├── strelka_process_vcf.cwl │ │ ├── trimming_options.yml │ │ ├── varscan.cwl │ │ ├── varscan_pre_and_post_processing.cwl │ │ ├── vcf_readcount_annotator.cwl │ │ ├── vep_custom_annotation.yml │ │ └── vt_decompose.cwl │ │ ├── tools │ │ ├── add_strelka_gt.cwl │ │ ├── add_vep_fields_to_table.cwl │ │ ├── apply_bqsr.cwl │ │ ├── bam_readcount.cwl │ │ ├── bam_to_bigwig.cwl │ │ ├── bam_to_cram.cwl │ │ ├── bam_to_fastq.cwl │ │ ├── bgzip.cwl │ │ ├── bqsr.cwl │ │ ├── cat_all.cwl │ │ ├── cat_out.cwl │ │ ├── cnvkit_batch.cwl │ │ ├── collect_alignment_summary_metrics.cwl │ │ ├── collect_hs_metrics.cwl │ │ ├── collect_insert_size_metrics.cwl │ │ ├── combine_variants.cwl │ │ ├── concordance.cwl │ │ ├── docm_add_variants.cwl │ │ ├── docm_gatk_haplotype_caller.cwl │ │ ├── extract_hla_alleles.cwl │ │ ├── filter_known_variants.cwl │ │ ├── filter_vcf_cle.cwl │ │ ├── filter_vcf_coding_variant.cwl │ │ ├── filter_vcf_custom_allele_freq.cwl │ │ ├── filter_vcf_depth.cwl │ │ ├── filter_vcf_docm.cwl │ │ ├── filter_vcf_mapq0.cwl │ │ ├── filter_vcf_somatic_llr.cwl │ │ ├── fp_filter.cwl │ │ ├── gatk_haplotype_caller.cwl │ │ ├── generate_qc_metrics.cwl │ │ ├── hisat2_align.cwl │ │ ├── hla_consensus.cwl │ │ ├── immuno_input.yaml │ │ ├── index_bam.cwl │ │ ├── index_cram.cwl │ │ ├── index_vcf.cwl │ │ ├── intersect_known_variants.cwl │ │ ├── interval_list_expand.cwl │ │ ├── intervals_to_bed.cwl │ │ ├── kallisto.cwl │ │ ├── manta_somatic.cwl │ │ ├── mark_duplicates_and_sort.cwl │ │ ├── merge_bams.cwl │ │ ├── merge_vcf.cwl │ │ ├── mutect.cwl │ │ ├── name_sort.cwl │ │ ├── normalize_variants.cwl │ │ ├── optitype_dna.cwl │ │ ├── picard_merge_vcfs.cwl │ │ ├── pindel.cwl │ │ ├── pindel_cat.cwl │ │ ├── pindel_somatic_filter.cwl │ │ ├── pvacseq.cwl │ │ ├── pvacseq_combine_variants.cwl │ │ ├── read_backed_phasing.cwl │ │ ├── remove_end_tags.cwl │ │ ├── replace_vcf_sample_name.cwl │ │ ├── samtools_flagstat.cwl │ │ ├── samtools_sort.cwl │ │ ├── select_variants.cwl │ │ ├── sequence_align_and_tag.cwl │ │ ├── sequence_data.yml │ │ ├── set_filter_status.cwl │ │ ├── sort_vcf.cwl │ │ ├── split_interval_list.cwl │ │ ├── split_interval_list_to_bed.cwl │ │ ├── staged_rename.cwl │ │ ├── strelka.cwl │ │ ├── stringtie.cwl │ │ ├── transcript_to_gene.cwl │ │ ├── trim_fastq.cwl │ │ ├── trimming_options.yml │ │ ├── variants_to_table.cwl │ │ ├── varscan_process_somatic.cwl │ │ ├── varscan_somatic.cwl │ │ ├── vcf_expression_annotator.cwl │ │ ├── vcf_readcount_annotator.cwl │ │ ├── vcf_sanitize.cwl │ │ ├── vep.cwl │ │ ├── vep_custom_annotation.yml │ │ ├── verify_bam_id.cwl │ │ └── vt_decompose.cwl │ │ └── types │ │ ├── labelled_file.yml │ │ ├── sequence_data.yml │ │ ├── trimming_options.yml │ │ └── vep_custom_annotation.yml ├── bcbio │ └── dnanexus │ │ ├── bcbio_system-dnanexus.yaml │ │ ├── clean_dnanexus.sh │ │ ├── gvcf-joint-workflow │ │ ├── main-gvcf-joint-samples.json │ │ ├── main-gvcf-joint.cwl │ │ ├── main-gvcf-joint.cwl.json │ │ ├── main-gvcf-joint_input.yaml │ │ ├── steps │ │ │ ├── alignment_to_rec.cwl │ │ │ ├── batch_for_jointvc.cwl │ │ │ ├── batch_for_variantcall.cwl │ │ │ ├── combine_sample_regions.cwl │ │ │ ├── compare_to_rm.cwl │ │ │ ├── concat_batch_variantcalls.cwl │ │ │ ├── concat_batch_variantcalls_jointvc.cwl │ │ │ ├── finalize_jointvc.cwl │ │ │ ├── get_parallel_regions.cwl │ │ │ ├── get_parallel_regions_jointvc.cwl │ │ │ ├── merge_split_alignments.cwl │ │ │ ├── multiqc_summary.cwl │ │ │ ├── pipeline_summary.cwl │ │ │ ├── postprocess_alignment.cwl │ │ │ ├── postprocess_alignment_to_rec.cwl │ │ │ ├── postprocess_variants.cwl │ │ │ ├── prep_align_inputs.cwl │ │ │ ├── prep_samples.cwl │ │ │ ├── prep_samples_to_rec.cwl │ │ │ ├── process_alignment.cwl │ │ │ ├── qc_to_rec.cwl │ │ │ ├── run_jointvc.cwl │ │ │ ├── summarize_vc.cwl │ │ │ └── variantcall_batch_region.cwl │ │ ├── wf-alignment.cwl │ │ ├── wf-jointcall.cwl │ │ └── wf-variantcall.cwl │ │ ├── gvcf-joint.yaml │ │ ├── run_compile_workflow.sh │ │ ├── run_dnanexus.sh │ │ └── run_generate_cwl.sh ├── clamms_call_cnvs │ ├── clamms_call_cnvs.cwl │ ├── clamms_call_cnvs.cwl.json │ └── clamms_call_cnvs_input.yaml ├── clamms_compute_windows │ ├── clamms_compute_windows.cwl │ ├── clamms_compute_windows.cwl.json │ └── clamms_compute_windows_input.yaml ├── clamms_fit_models │ ├── clamms_fit_models.cwl │ ├── clamms_fit_models.cwl.json │ └── clamms_fit_models_input.yaml ├── clamms_normalize_coverage │ ├── clamms_normalize_coverage.cwl │ ├── clamms_normalize_coverage.cwl.json │ └── clamms_normalize_coverage_input.yaml ├── fermikit │ ├── fermikit.cwl │ ├── fermikit.cwl.json │ └── fermikit_input.yaml ├── nci │ └── ccbr-rna-seq-de-310.cwl.json ├── opencravat │ ├── oc.cwl │ ├── oc.cwl.json │ └── oc_input.yaml └── run-dten │ └── cwl │ ├── README.md │ ├── build-store-networks-with-params.cwl │ ├── cwl │ ├── synapse-create-tool.cwl │ ├── synapse-get-annotations-tool.cwl │ ├── synapse-get-sts-tool.cwl │ ├── synapse-get-tool.cwl │ ├── synapse-query-tool.cwl │ ├── synapse-set-annotations-tool.cwl │ ├── synapse-store-tool.cwl │ └── synapse-sync-to-synapse-tool.cwl │ ├── dten-test.yml │ ├── dten-tissue.yml │ ├── network-and-store.cwl │ ├── run-dten-from-query-list.cwl │ ├── run-dten-from-table.cwl │ ├── run-dten.cwl │ ├── run-dten.cwl.json │ ├── run-dten_input.yaml │ ├── run-nf2.yml │ ├── sample-dten-from-fv.cwl │ ├── steps │ ├── get-mv-samples.cwl │ ├── make-net-name.cwl │ ├── proteins-from-genes.cwl │ ├── run-meta-analysis.cwl │ ├── run-network-with-params.cwl │ └── store-tables.cwl │ ├── tcga-sample.yml │ └── tcga-unique.yml ├── docker ├── biocontainers.wdl ├── biocontainers_extras.json ├── broad_genomics.wdl ├── broad_genomics_input.json ├── dockerhub_test_image │ ├── Dockerfile │ └── Makefile ├── dynamic_docker_image.wdl ├── dynamic_docker_image_input.json ├── dynamic_docker_image_results.json ├── ecr_docker.wdl ├── ecr_docker_extras.json ├── ecr_docker_input.json ├── native_docker_file_image.wdl ├── native_docker_file_image_gzip.wdl ├── native_docker_file_image_gzip_results.json ├── native_docker_file_image_results.json ├── private_registry.wdl ├── private_registry_extras.json ├── private_registry_input.json ├── private_registry_results.json ├── samtools_count.wdl └── samtools_count_input.json ├── draft2 ├── advanced.wdl ├── advanced_input.json ├── advanced_results.json ├── array_add.wdl ├── array_mul.wdl ├── bad_status.wdl ├── bad_status2.wdl ├── bad_status2_input.json ├── bad_status_input.json ├── call_native.wdl ├── call_native_input.json ├── call_native_results.json ├── call_with_defaults1.wdl ├── call_with_defaults1_input.json ├── call_with_defaults1_results.json ├── call_with_defaults2.wdl ├── call_with_defaults2_input.json ├── call_with_defaults2_results.json ├── conditionals2.wdl ├── conditionals2_input.json ├── conditionals2_results.json ├── conditionals_base.wdl ├── conditionals_base_input.json ├── conditionals_base_results.json ├── files.wdl ├── files_input.json ├── files_input_cromwell.json ├── files_results.json ├── files_with_the_same_name.wdl ├── files_with_the_same_name_input.json ├── files_with_the_same_name_results.json ├── hello.wdl ├── hello_extras.json ├── hello_input.json ├── hello_results.json ├── just_fail_wf.wdl ├── library.wdl ├── library_math.wdl ├── library_string.wdl ├── library_sys_call.wdl ├── modulo.wdl ├── modulo_input.json ├── modulo_results.json ├── movies.wdl ├── movies_input.json ├── movies_results.json ├── multiple_imports.wdl ├── multiple_imports_input.json ├── multiple_imports_results.json ├── shapes.wdl ├── shapes_input.json ├── shapes_result.json ├── subblocks.wdl ├── subblocks2.wdl ├── subblocks2_input.json ├── subblocks2_results.json ├── subblocks_input.json ├── subblocks_results.json ├── var_type_change.wdl ├── var_type_change_input.json └── var_type_change_results.json ├── imports ├── A.wdl ├── A_inputs.json ├── lib │ └── library.wdl └── multi_level │ ├── dxwdl │ ├── main.wdl │ └── util │ ├── other.wdl │ └── util.wdl ├── input_file ├── echo_pairs.wdl ├── echo_pairs_input.json ├── echo_pairs_results.json ├── population.wdl ├── population_input.json └── population_results.json ├── local ├── X.txt ├── Y.txt └── Z.txt ├── manifest ├── apps_1269_1270_unqualified_ids_manifest.wdl ├── apps_1269_1270_unqualified_ids_manifest_input.json ├── complex_manifest.wdl ├── complex_manifest_input.json ├── simple_manifest.wdl ├── simple_manifest_input.json ├── tumor_normal.wdl ├── view_and_count_manifest.wdl └── view_and_count_manifest_input.json ├── multi_region └── trivial.wdl ├── multi_user ├── global_wf_from_wdl.wdl ├── global_wf_from_wdl_multiply │ ├── Readme.md │ ├── dxapp.json │ └── src │ │ └── global_wf_from_wdl_multiply.py └── global_wf_from_wdl_sub.wdl ├── nested ├── apps_1128_frag_native_instance_type_override.wdl ├── apps_1128_frag_native_instance_type_override_input.json ├── apps_1128_frag_native_instance_type_override_results.json ├── apps_1177_native_indirect_override.wdl ├── apps_1177_native_indirect_override_input.json ├── apps_1177_native_indirect_override_results.json ├── apps_1197_native_frag_default.wdl ├── apps_1197_native_frag_default_input.json ├── apps_1197_native_frag_default_results.json ├── apps_612.wdl ├── apps_612_input.json ├── apps_612_results.json ├── four_levels.wdl ├── four_levels_files.wdl ├── four_levels_input.json ├── four_levels_results.json ├── nested_optional.wdl ├── nested_optional_input.json ├── nested_optional_results.json ├── nested_scatter.wdl ├── nested_scatter2.wdl ├── nested_scatter2_input.json ├── nested_scatter_results.json ├── nested_wf.wdl ├── param_passing.wdl ├── param_passing_input.json ├── param_passing_results.json ├── three_levels.wdl ├── three_levels_input.json ├── three_levels_results.json ├── two_levels.wdl ├── two_levels_input.json └── two_levels_results.json ├── single_tasks ├── DiskSpace2.wdl ├── DiskSpace2_input.json ├── README.md ├── add3.wdl ├── add3_input.json ├── add3_results.json ├── diff2files.wdl ├── diff2files_input.json ├── diff2files_results.json ├── docker_retry.wdl ├── echo_line_split.wdl ├── echo_line_split_results.json ├── empty_stdout.wdl ├── empty_stdout_input.json ├── empty_stdout_results.json ├── find_fastq_in_folder.wdl ├── find_fastq_in_folder_input.json ├── find_fastq_in_folder_results.json ├── multi_line.wdl ├── opt_array.wdl ├── opt_array_input.json ├── python_task_fail.wdl ├── python_task_fail_docker.wdl ├── python_task_fail_docker_results.json ├── python_task_fail_results.json ├── sort_file.wdl ├── sort_file_input.json ├── stream_diff_v1.wdl ├── stream_diff_v1_input.json ├── stream_diff_v1_results.json ├── symlinks_wc.wdl ├── symlinks_wc_extras.json ├── symlinks_wc_input.json ├── symlinks_wc_results.json ├── unzip_files.wdl └── unzip_files_input.json ├── special_flags ├── add2.wdl ├── add2_extras.json ├── add2_input.json ├── add2_results.json ├── add_many.wdl ├── add_many_input.json ├── add_many_results.json ├── inc_range.wdl └── inc_range_results.json ├── struct ├── array_structs.wdl ├── array_structs_input.json ├── array_structs_results.json ├── runtime_vs_static_type.wdl ├── runtime_vs_static_type_result.json ├── struct_deref.wdl ├── struct_deref_input.json ├── struct_imported_twice │ ├── Block_results.json │ ├── Blorf_input.json │ ├── bloop.wdl │ ├── blorf.wdl │ └── foo_def.wdl ├── type_mismatch.wdl ├── wf_person.wdl ├── wf_person_input.json └── wf_person_results.json ├── subworkflows ├── check_route.wdl ├── inner.wdl ├── inner_input.json ├── inner_results.json ├── outer.wdl ├── outer_input.json ├── outer_results.json ├── subworkflow_with_defaults.wdl ├── trains.wdl ├── trains_input.json ├── trains_results.json ├── workflow_with_subworkflow.wdl └── workflow_with_subworkflow_results.json ├── upload ├── upload_wait.wdl ├── upload_workflow_files.wdl └── upload_workflow_files_results.json ├── wdl_1_0 ├── .gitignore ├── apps_1318_nested.wdl ├── basename-fields.wdl ├── booleam_param_results.json ├── boolean_param.wdl ├── bwa_mem.wdl ├── bwa_mem_input.json ├── call_level2.wdl ├── call_level2_input.json ├── call_native_app.wdl ├── call_native_app_input.json ├── call_native_app_results.json ├── call_native_results.json ├── call_native_v1.wdl ├── call_native_v1_input.json ├── cast.wdl ├── cast_input.json ├── cast_results.json ├── dict.wdl ├── dict_results.json ├── download_from_container.wdl ├── empty_array.wdl ├── empty_array_input.json ├── empty_array_results.json ├── environment_passing_deep_nesting.wdl ├── environment_passing_deep_nesting_input.json ├── environment_passing_deep_nesting_results.json ├── instance_types.wdl ├── instance_types_extras.json ├── instance_types_input.json ├── instance_types_results.json ├── linear.wdl ├── linear_no_expressions.wdl ├── linear_no_expressions_results.json ├── linear_results.json ├── map_file_key.wdl ├── map_file_key_input.json ├── missing_optional_output_file.wdl ├── missing_optional_output_file_results.json ├── optional_output.wdl ├── optionals.wdl ├── optionals2.wdl ├── optionals3.wdl ├── optionals3_input.json ├── optionals3_results.json ├── optionals_input.json ├── optionals_results.json ├── path_not_taken.wdl ├── path_not_taken_results.json ├── scatter_subworkflow_with_optional.wdl ├── simple_scatter.wdl ├── simple_scatter_input.json ├── simple_scatter_results.json ├── spaces_in_file_paths.wdl ├── streaming_inputs.wdl ├── streaming_inputs_input.json ├── streaming_inputs_output.json ├── strings.wdl ├── strings_results.json ├── top_wf.wdl ├── top_wf_input.json ├── unpassed_default_arg.wdl ├── wf_with_input_expressions.wdl ├── wf_with_input_expressions_input.json ├── wf_with_input_expressions_results.json ├── wf_with_output_expressions.wdl ├── wf_with_output_expressions_input.json ├── wf_with_output_expressions_results.json └── yih_chii_workflow.wdl ├── wdl_1_1 ├── apps_847_scatter_empty.wdl ├── apps_847_scatter_empty_input.json ├── inputs_provided_optional.wdl ├── inputs_provided_optional_input.json ├── localization.wdl ├── optional_missing.wdl ├── optional_missing_input.json ├── structs.wdl ├── v1_1_dict.wdl └── v1_1_dict_results.json └── wdl_2_0 ├── apps_1421_dir_output.wdl └── apps_1421_dir_output_extras.json /compiler/src/main/resources/logback.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /compiler/src/main/resources/templates/static_applet_script.ssp: -------------------------------------------------------------------------------- 1 | <%@ val dockerPreamble: Option[String] %> 2 | set -exo pipefail 3 | 4 | ${include("applet_script.ssp")} 5 | 6 | main() { 7 | body 8 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/bugs/apps-573_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_573.out": "1^I1$\n2\\t2$\n3\\^I3$\n4\\\\t4$" 3 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/bugs/subwf.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | workflow foo { 4 | input { 5 | Array[File]+ inp 6 | } 7 | output { 8 | Array[File]+ out = inp 9 | } 10 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/Readme.wf_readme.add.md: -------------------------------------------------------------------------------- 1 | This is the readme for the wf_linear add task. -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/Readme.wf_readme.wf_readme.md: -------------------------------------------------------------------------------- 1 | This is the readme for the wf_linear workflow. -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/extras/apps_1858_top_wf_attrs.json: -------------------------------------------------------------------------------- 1 | { 2 | "per_workflow_dx_attributes": { 3 | "apps_1858_tat_wf": { 4 | "treeTurnaroundTimeThreshold": 2 5 | } 6 | } 7 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/extras/apps_2477_default_task_on_demand.json: -------------------------------------------------------------------------------- 1 | { 2 | "defaultTaskDxAttributes": { 3 | "runSpec": { 4 | "headJobOnDemand": true 5 | } 6 | } 7 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/extras/extras_custom_reorg.json: -------------------------------------------------------------------------------- 1 | { 2 | "custom_reorg": { 3 | "app_id": "applet-Fg623fj0jy8q7jjv9xV6q5fQ", 4 | "conf": null 5 | } 6 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/imports/A_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "A.x" : 1, 3 | "A.y" : 2 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/compiler/imports/subworkflow.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | import "lib.wdl" 4 | 5 | workflow foo { 6 | call lib.bar 7 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/draft2/output_only.wdl: -------------------------------------------------------------------------------- 1 | workflow output_only { 2 | output { 3 | Int notUsed = 0 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /compiler/src/test/resources/frag_runner/ma.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_args.y" : 5 3 | } 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/L3.wdl: -------------------------------------------------------------------------------- 1 | import "L2.wdl" as lib 2 | 3 | workflow L3 { 4 | Int x 5 | Int y 6 | 7 | call lib.L2 { input: x = x, y = y } 8 | } 9 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/L3_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "L3.x" : 1, 3 | "L2.y" : 2, 4 | "subtract.x" : 3 5 | } 6 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/add_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "add.a" : 1, 3 | "add.b" : 2 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/bool-empty-inputbinding_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "bool-empty-inputbinding.flag": true, 3 | "bool-empty-inputbinding.args___py": "dx://file-GJ85b9j0yzZxbQ1Z1V5z98qZ" 4 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/dir_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir.indir": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/testdir/" 5 | } 6 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/echo-tool-packed_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/echo_pairs_input.json: -------------------------------------------------------------------------------- 1 | {"echo_pairs.pairs_of_words": 2 | [ 3 | ["hello", "world"], 4 | {"left" : "hello_again", "right" : "world_again"} 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/enum-string_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "enum-string.example_in": "string2" 3 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/map_argument_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "map_argument.names_and_phones": { 3 | "Gina" : 334320, 4 | "Chad" : 578333, 5 | "Valery" : 88339 6 | } 7 | } 8 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/map_input.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/compiler/src/test/resources/input_file/map_input.wdl -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/math_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "math.x" : 4 3 | } 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/math_inputs2.json: -------------------------------------------------------------------------------- 1 | { 2 | "math.x" : 4, 3 | "math.y" : 5 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/missing_args_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_args.flag" : true, 3 | "missing_args.prime" : 19, 4 | "missing_args.Add.b" : 3 5 | } 6 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/no_file_key_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "no_file_key.file_key": { 3 | "dx://dxCompiler_playground:/test_data/fileA": "this is string value" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/override_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "override.etl.b" : 5, 3 | "override.etl.c" : 9 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/population_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "population.start" : 0.8, 3 | "next_year.factor" : 3.4 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/population_top.wdl: -------------------------------------------------------------------------------- 1 | workflow population_top { 2 | call population{ input: start = 0.3 } 3 | } 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/runtime_override_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "runtime_override.s": "foo", 3 | "runtime_override.runtime.docker": "debian:latest", 4 | "runtime_override.runtime.cpu": 8 5 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/input_file/several_tasks_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "add.a" : 1, 3 | "add.b" : 2, 4 | "mul.a" : 5, 5 | "mul.b" : 3 6 | } 7 | -------------------------------------------------------------------------------- /compiler/src/test/resources/logback-test.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/manifest/simple_manifest_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_manifest.input_manifest___": { 3 | "s": "joe", 4 | "f": "dx://file-FGzzpkQ0ffPJX74548Vp6670" 5 | } 6 | } -------------------------------------------------------------------------------- /compiler/src/test/resources/nested/four_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.username" : "Alberta" 3 | } 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/nested/three_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.score" : 100 3 | } 4 | -------------------------------------------------------------------------------- /compiler/src/test/resources/struct/Person_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "myWorkflow.a" : { 3 | "name": "John", 4 | "age": 30 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /compiler/src/test/resources/struct/array_of_structs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "array_of_structs.words_to_say": [ 3 | {"word": "hello"}, 4 | {"word": "world"} 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /compiler/src/test/resources/struct/struct_imported_twice/file1.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | struct Foo { 4 | String bar 5 | } 6 | -------------------------------------------------------------------------------- /compiler/src/test/resources/subworkflows/trains_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "trains.prefixes" : ["xxx_", "yyy_"], 3 | "trains.ranges" : ["0--1000", "10000--88000"] 4 | } 5 | -------------------------------------------------------------------------------- /compiler/src/test/resources/util/empty_workflow.wdl: -------------------------------------------------------------------------------- 1 | workflow foo { 2 | } 3 | -------------------------------------------------------------------------------- /contrib/beginner_example/bam_chrom_counter_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "bam_chrom_counter.bam" : "dx://project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGV" 3 | } 4 | -------------------------------------------------------------------------------- /contrib/czi/README.md: -------------------------------------------------------------------------------- 1 | # README 2 | 3 | The scripts here were copied, with permission, from the [HumanCellAtlas project](https://github.com/HumanCellAtlas/skylab). 4 | -------------------------------------------------------------------------------- /core/src/main/resources/logback.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /core/src/test/resources/compiler/Readme.wf_readme.add.md: -------------------------------------------------------------------------------- 1 | This is the readme for the wf_linear add task. -------------------------------------------------------------------------------- /core/src/test/resources/compiler/Readme.wf_readme.wf_readme.md: -------------------------------------------------------------------------------- 1 | This is the readme for the wf_linear workflow. -------------------------------------------------------------------------------- /core/src/test/resources/compiler/extras/extras_custom_reorg.json: -------------------------------------------------------------------------------- 1 | { 2 | "custom_reorg": { 3 | "app_id": "applet-Fg623fj0jy8q7jjv9xV6q5fQ", 4 | "conf": null 5 | } 6 | } -------------------------------------------------------------------------------- /core/src/test/resources/compiler/imports/A_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "A.x" : 1, 3 | "A.y" : 2 4 | } 5 | -------------------------------------------------------------------------------- /core/src/test/resources/compiler/imports/subworkflow.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | import "lib.wdl" 4 | 5 | workflow foo { 6 | call lib.bar 7 | } -------------------------------------------------------------------------------- /core/src/test/resources/logback-test.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /core/src/test/resources/nested/four_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.username" : "Alberta" 3 | } 4 | -------------------------------------------------------------------------------- /core/src/test/resources/nested/three_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.score" : 100 3 | } 4 | -------------------------------------------------------------------------------- /core/src/test/resources/struct/Person_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "myWorkflow.a" : { 3 | "name": "John", 4 | "age": 30 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /core/src/test/resources/struct/array_of_structs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "array_of_structs.words_to_say": [ 3 | {"word": "hello"}, 4 | {"word": "world"} 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /core/src/test/resources/struct/struct_imported_twice/file1.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | struct Foo { 4 | String bar 5 | } 6 | -------------------------------------------------------------------------------- /core/src/test/resources/subworkflows/trains_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "trains.prefixes" : ["xxx_", "yyy_"], 3 | "trains.ranges" : ["0--1000", "10000--88000"] 4 | } 5 | -------------------------------------------------------------------------------- /core/src/test/resources/util/empty_workflow.wdl: -------------------------------------------------------------------------------- 1 | workflow foo { 2 | } 3 | -------------------------------------------------------------------------------- /cwl_runner/dx_cwl_runner/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.2.1" 2 | -------------------------------------------------------------------------------- /doc/bam_chrom_counter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/bam_chrom_counter.png -------------------------------------------------------------------------------- /doc/images/linear.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/linear.png -------------------------------------------------------------------------------- /doc/images/linear2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/linear2.png -------------------------------------------------------------------------------- /doc/images/mul-loop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/mul-loop.png -------------------------------------------------------------------------------- /doc/images/mul_loop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/mul_loop.png -------------------------------------------------------------------------------- /doc/images/optionals.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/optionals.png -------------------------------------------------------------------------------- /doc/images/two_levels.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/doc/images/two_levels.png -------------------------------------------------------------------------------- /dxcint/config/cwl_cromwell.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /dxcint/config/cwl_tools.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /dxcint/config/cwl_workflows.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /dxcint/config/uncategorized.json: -------------------------------------------------------------------------------- 1 | {"expected_failure": ["docker_retry", "argument_list_too_long"]} -------------------------------------------------------------------------------- /dxcint/dependencies/config/awscli.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "awscliv2", 3 | "languages": ["wdl", "cwl"], 4 | "version": "2.2.0", 5 | "package_manager": "pip" 6 | } -------------------------------------------------------------------------------- /dxcint/dependencies/config/cwltool.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "cwltool", 3 | "languages": ["cwl"], 4 | "version": "3.1.20250110105449", 5 | "package_manager": "pip" 6 | } -------------------------------------------------------------------------------- /dxcint/dependencies/config/schema-salad.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "schema-salad", 3 | "languages": ["cwl"], 4 | "version": "8.8.20250205075315", 5 | "package_manager": "pip" 6 | } -------------------------------------------------------------------------------- /dxcint/dxcint/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = "0.1.0" 2 | -------------------------------------------------------------------------------- /dxcint/dxcint/constants.py: -------------------------------------------------------------------------------- 1 | DEFAULT_INSTANCE_TYPE = "mem1_ssd1_v2_x4" 2 | DEFAULT_TEST_PROJECT = "dxCompiler_playground" 3 | DEFAULT_RUN_KWARGS = {"ignore_reuse": True} 4 | -------------------------------------------------------------------------------- /dxcint/dxcint/mixins/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/dxcint/dxcint/mixins/__init__.py -------------------------------------------------------------------------------- /dxcint/dxcint/testclasses/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/dxcint/dxcint/testclasses/__init__.py -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/DiskSpace2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "DiskSpace2.fruits" : "dx://dxCompiler_playground:/test_data/fileB" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/apps_1052_optional_compound_input_wdl10_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_compound_input_wdl10.t1" : {"inner": {}} 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/apps_847_scatter_empty_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_filter.samples_to_exclude": [] 3 | } -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/apps_936_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_936.foo": { 3 | "docker_image": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-G66qpGj0yzZq02K9313pJg5G" 4 | } 5 | } -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/call_level2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_level2.run_name" : "Cherry blossom" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/forkjoin_input.json: -------------------------------------------------------------------------------- 1 | { 2 | } -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/lots_of_inputs_input.json: -------------------------------------------------------------------------------- 1 | { "lots_of_inputs.how_many_is_lots": 400 } 2 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/map_file_key_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "map_file_key.file_key": { 3 | "dx://dxCompiler_playground:/test_data/fileA": "this is string value" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/nested_lookups.inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_lookups.needs_wf_input.i": 2050 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/no_task_no_output_delete.wdl: -------------------------------------------------------------------------------- 1 | workflow no_task_no_output_delete { 2 | output { 3 | Int notUsed = 0 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/opt_array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "opt_array.b" : ["dx://dxCompiler_playground:/test_data/fileA", "dx://dxCompiler_playground:/test_data/fileB"] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/recimp_nosubwf_outer.wdl: -------------------------------------------------------------------------------- 1 | import "recimp_nosubwf_inner.wdl" as inner 2 | 3 | # Nothing at all 4 | task rins_outer { 5 | command {} 6 | output {} 7 | } 8 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/samtools_count_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "samtools_count.bam" : "dx://dxCompiler_playground:/test_data/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/sort_file_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "sort_file.src" : "dx://dxCompiler_playground:/test_data/fileA", 3 | "sort_file.basename" : "happyDays" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/subworkflow_wt_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subwf_wt.is" : [1,2,3,4,5,6,7,8,9] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/analysis_finished/top_wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "top_wf.arr" : ["Archie"] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/app_extern_expected_output/call_native_app_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_native_app.my_name" : "Wilbert" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/app_extern_expected_output/call_native_app_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_native_app.result" : "hello Wilbert" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_failure/apps_1014.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | task apps_1014 { 4 | command <<< 5 | exit 1 6 | >>> 7 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_failure/just_fail_wf.wdl: -------------------------------------------------------------------------------- 1 | workflow just_fail_wf { 2 | call just_fail 3 | } 4 | 5 | task just_fail { 6 | command { 7 | exit 1 8 | } 9 | } 10 | -------------------------------------------------------------------------------- /dxcint/resources/expected_flags/add2_extras.json: -------------------------------------------------------------------------------- 1 | { 2 | "ignoreReuse": true 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_flags/add2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "add2.a" : 10, 3 | "add2.b" : 11 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_flags/add2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "add2.add2.ignoreReuse" : true 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/add3_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "add3.a": 1, 3 | "add3.b": 2, 4 | "add3.c": 4 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/add3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "add3.result" : 7 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_1052_optional_block_inputs_wdl10_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_block_inputs_wdl10.filesCount": 3 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_1052_optional_block_inputs_wdl11_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_block_inputs_wdl11.filesCount": 3 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_378_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_378.sample_names_out": ["a"], 3 | "apps_378.sample_types_out": ["foo"] 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_573_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_573.out": "1^I1$\n2\\t2$\n3\\^I3$\n4\\\\t4$" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_579_boolean_flag_expr_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_579_boolean_flag_expr.out" : "x" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_579_string_substitution_expr_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_579_string_substitution_expr.out" : "aa" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_612_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_612.b": true, 3 | "apps_612.x": "hello" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/apps_612_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_612.out": "hello" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/call_with_defaults2_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/checkpointing_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "checkpointing.preempted": "GOTPREEMPTED" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/conditionals2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals2.flag" : true 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/conditionals2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals2.mul": [5, 1, 4], 3 | "conditionals2.add2_r": 5 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/conditionals_base_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/conditionals_base_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals_base.results" : [1, 100], 3 | "conditionals_base.nea" : [5,7] 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/custom_entrypoint_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "custom_entrypoint.hello": "hello world" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/diff2files_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "diff2files.a" : "dx://dxCompiler_playground:/test_data/fileA", 3 | "diff2files.b" : "dx://dxCompiler_playground:/test_data/fileC" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/diff2files_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "diff2files.result" : 5 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/docker_image_cache_false_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "docker_image_cache_false.is_docker_image_cache_disk_mounted": false 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/docker_image_cache_unspecified_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "docker_image_cache_unspecified.is_docker_image_cache_disk_mounted": false 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/dynamic_docker_image_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dynamic_docker_image.docker_dxfile" : "dx:///ubuntu-bionic.tar" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/dynamic_docker_image_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "dynamic_docker_image.cat": "hello world" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/echo_line_split_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_line_split.results" : "1 hello wdl\n2 hello wdl\n3 hello wdl" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/echo_pairs_input.json: -------------------------------------------------------------------------------- 1 | {"echo_pairs.pairs_of_words": 2 | [ 3 | ["alpine", "env"], 4 | ["shasta", "lake"] 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/echo_pairs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_pairs.all_echoed_words" : [ "alpine env", "shasta lake"] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/empty_array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_array.names": [] 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/empty_array_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_array.greetings": [], 3 | "empty_array.num_names": 0 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/empty_stdout_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_stdout.result" : "" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/empty_string_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_string.hello2": "" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/environment_passing_deep_nesting_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_passing_deep_nesting.verify" : true 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/environment_passing_deep_nesting_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_passing_deep_nesting.result" : 7 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/files_with_the_same_name_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "files_with_the_same_name.result" : 114 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/four_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.username" : "Alberta" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/four_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.r2": [null, "hello_clease"], 3 | "four_levels.r1": null, 4 | "four_levels.r3": ["john_Alberta", null] 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/linear_no_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "linear_no_expressions.r1" : 9, 3 | "linear_no_expressions.r2" : 15, 4 | "linear_no_expressions.r3" : 25 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/linear_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "linear.result" : 63 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/missing_optional_output_file_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_optional_output_file.a" : { 3 | "___": [null, null] 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/modulo_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "modulo.n": 7 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/modulo_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "modulo.mulr": [0, 2, 4, 6, 1, 3, 5], 3 | "modulo.addr": [3, 4, 5, 6, 0, 1, 2] 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/movies_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "movies.m_name" : "The diving bell and the butterfly" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/movies_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "movies.stage-0.score": 0.6000000000000001 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/multiline_command_line_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "multiline_command_line.stage-0.ab": "ab" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/multiple_imports_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/multiple_imports_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "multiple_imports.r_mul" : 40, 3 | "multiple_imports.r_con" : "carrots_coconut" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/native_docker_file_image_gzip_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "native_docker_file_image_gzip.result" : "bionic" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/native_docker_file_image_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "native_docker_file_image.result" : "bionic" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/nested_optional_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_optional.s": "hello" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/nested_optional_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_optional.outstr": "hello", 3 | "nested_optional.outstr2": "hello" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/nested_pairs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_pairs.messages": ["hello goodbye", "up down"], 3 | "nested_pairs.names": ["a", "b"] 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/optionals3_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /dxcint/resources/expected_output/optionals3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals3.k": [1, 2] 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/outer_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "outer.lane" : "Penny" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/outer_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "outer.o" : "Penny" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/output_redirection_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "output_redirection.stage-0.stdout": "should be on stdout", 3 | "output_redirection.stage-0.stderr": "should be on stderr" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/param_passing_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "param_passing.num" : 10, 3 | "param_passing.flag" : true 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/param_passing_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "param_passing.r1" : [13, 14, 15], 3 | "param_passing.r2" : 14 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/passingfiles_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "passingfiles.contents_out": "small file contents", 3 | "passingfiles.contentsAlt_out": "small file contents" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/simple_if_workflow_outputs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_if_workflow_outputs.rmf": null, 3 | "simple_if_workflow_outputs.rmt": "done" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/single_to_array_conversion_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "single_to_array_conversion.stage-2.listFiles___result": "hello" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/stream_diff_v1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "stream_diff_v1.result" : 282 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/streaming_inputs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "streaming_inputs.r1": "foo", 3 | "streaming_inputs.r2": "bar" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/sub_workflow_hello_world_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "sub_workflow_hello_world.main_output": "Hello sub world!" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/subblocks2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks2.numbers" : [ 1, 2, 4 ] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/subblocks2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks2.ms": [4, 5, 7] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/subblocks_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks.numbers" : [ 1, 2, 4 ] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/subblocks_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks.mul_a": [2, 4, 1], 3 | "subblocks.add_a": [2, 3, 5], 4 | "subblocks.sub_a": [1, 2, 4] 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/subworkflow_with_task_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "subworkflow_with_task.res_string_subtask_input": "test-string-2" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/three_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.score" : 100 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/three_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.result1" : 14, 3 | "three_levels.result2" : null 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/two_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "two_levels.a" : [4, 5, 6], 3 | "two_levels.b" : 4, 4 | "two_levels.c" : 2 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/v1_1_dict_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "v1_1_dict.result" : [6, 15] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/var_type_change_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "var_type_change.result": ["Banana is good to eat", 3 | "Apple is good to eat"] 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/wf_with_input_expressions_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_input_expressions.f": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-Fgv1zP00ffP0FVk59X8j9zBX" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/wf_with_input_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_input_expressions.x1": "X.txt", 3 | "wf_with_input_expressions.x2": "X.txt" 4 | } -------------------------------------------------------------------------------- /dxcint/resources/expected_output/wf_with_output_expressions_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_output_expressions.a" : 1, 3 | "wf_with_output_expressions.b" : "mensch" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/wf_with_output_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_output_expressions.x" : 2, 3 | "wf_with_output_expressions.x2" : "mensch_mensch" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/expected_output/write_lines_bug_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "write_lines_bug.strings": [ 3 | "/home/dnanexus/inputs/input0/fileA", 4 | "/home/dnanexus/inputs/input0/fileB" 5 | ] 6 | } -------------------------------------------------------------------------------- /dxcint/resources/extras_analysis_finished/biocontainers_extras.json: -------------------------------------------------------------------------------- 1 | { 2 | "default_runtime_attributes" : { 3 | "docker" : "biocontainers/samtools:v1.7.0_cv4" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/extras_analysis_finished/ecr_docker_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "ecr_docker.s": "hello" 3 | } -------------------------------------------------------------------------------- /dxcint/resources/extras_expected_flags/apps_2478_headJobOnDemand_subjob_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_2478_headJobOnDemand_subjob.fruits" : "dx://dxCompiler_playground:/test_data/fileB" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/extras_expected_output/instance_types_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "instance_types.i" : 15, 3 | "instance_types.fruits" : "dx://dxCompiler_playground:/test_data/fileB" 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/extras_expected_output/private_registry_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "private_registry.result" : "Major Major" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/extras_expected_output/symlinks_wc_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "symlinks_wc.a" : "dx://dxCompiler_playground:/test_data/symlinks/1000G_2504_high_coverage.sequence.index" 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/extras_expected_output/symlinks_wc_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "symlinks_wc.result" : 2528 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/imports/structs.wdl: -------------------------------------------------------------------------------- 1 | version 1.1 2 | 3 | struct MyStructDB { 4 | String database_name 5 | Int? num_columns 6 | Int num_rows 7 | String? value_types 8 | } 9 | 10 | -------------------------------------------------------------------------------- /dxcint/resources/reorg_expected_output/dict_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "dict.result" : ["carrots", "oranges", "pear", "coconut" ] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/static_pinned_instance_expected_failure/diskspace_exhauster_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "diskspace_exhauster.count": 64 3 | } -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/array_structs_input.json: -------------------------------------------------------------------------------- 1 | {"array_structs.words_to_say": [ 2 | {"word": "hello"}, 3 | {"word": "world"} 4 | ]} 5 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/array_structs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "array_structs.out_words" : ["hello", "world"] 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/call_with_defaults1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_with_defaults1.x" : 1, 3 | "call_with_defaults1.flag" : true 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/call_with_defaults1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_with_defaults1.result" : 4 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/cast_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cast.i": 7, 3 | "cast.s": "French horn", 4 | "cast.foo": "dx://dxCompiler_playground:/test_data/fileA" 5 | } 6 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/cast_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cast.SumArray_result": 7 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/optionals_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals.flag": true 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/optionals_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals.r_mi1": 13, 3 | "optionals.r_mi2": 13, 4 | "optionals.r_mi3": 13, 5 | "optionals.r_mi4": 13 6 | } 7 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/shapes_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "shapes.num" : 3 3 | } 4 | -------------------------------------------------------------------------------- /dxcint/resources/unlocked_expected_output/shapes_result.json: -------------------------------------------------------------------------------- 1 | { 2 | "shapes.r1" : [0, 1, 4], 3 | "shapes.r2" : 1000 4 | } 5 | -------------------------------------------------------------------------------- /dxcint/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/dxcint/tests/__init__.py -------------------------------------------------------------------------------- /dxcint/tests/fixtures/config/medium.json: -------------------------------------------------------------------------------- 1 | {"mock_category": ["mock_1", "mock_2"]} -------------------------------------------------------------------------------- /dxcint/tests/fixtures/dependencies/config/mock_dependency.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "pytest", 3 | "languages": ["wdl", "cwl"], 4 | "version": "7.2.2", 5 | "package_manager": "pip" 6 | } -------------------------------------------------------------------------------- /dxcint/tests/fixtures/new_tests/mock_test.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/dxcint/tests/fixtures/new_tests/mock_test.wdl -------------------------------------------------------------------------------- /dxcint/tests/fixtures/resources/mock_category/efm.wdl: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /dxcint/tests/fixtures/resources/mock_category/mock_1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "mock_1.in_1": "Hello World!" 3 | } -------------------------------------------------------------------------------- /dxcint/tests/fixtures/resources/mock_category/mock_1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "mock_1.out": "Hello World!" 3 | } -------------------------------------------------------------------------------- /dxcint/tests/fixtures/resources/mock_category/mock_2.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/dxcint/tests/fixtures/resources/mock_category/mock_2.cwl 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-------------------------------------------------------------------------------- 1 | { 2 | "missing_args.y" : 5 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/logback-test.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/nested/four_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.username" : "Alberta" 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/nested/three_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.score" : 100 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/Person2_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/Person2_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "result" : "hello my name is John and I am 30 years old" 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/add_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "a": 1, 3 | "b" : 2 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/add_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "result": 3 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/cast_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "a" : 5, 3 | "b" : true 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/cast_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "result_a": "5", 3 | "result_b" : "true" 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/cgrep_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "pattern" : "snow", 3 | "in_file" : "manuscript.txt" 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/cgrep_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "count" : 3 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/empty_command_section_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "a": 1, 3 | "b" : 2 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/expressions_runtime_section_2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "base_mem_mb" : 2048, 3 | "disk_gb" : 512 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/expressions_runtime_section_2_output.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/expressions_runtime_section_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "mem_mb" : 1000, 3 | "disks" : "4" 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/expressions_runtime_section_output.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/float_arith_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "x" : 1.0 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/float_arith_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "x_round" : 1, 3 | "y_floor" : 2, 4 | "z_ceil" : 1 5 | } 6 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/manuscript.txt: -------------------------------------------------------------------------------- 1 | snow is found in the acrtic. 2 | There are snow hares, 3 | and snow shoes. 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/ps.wdl: -------------------------------------------------------------------------------- 1 | task ps { 2 | command { 3 | ps aux | head -c 1000 4 | } 5 | output { 6 | String procs = read_string(stdout()) 7 | } 8 | } 9 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/python_heredoc_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "A": "python_heredoc.wdl", 3 | "B": "python_heredoc.wdl" 4 | } -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/read_tsv_x_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/spaces_in_file_paths.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/sub_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "a" : 8, 3 | "b" : 3 4 | } 5 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/sub_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "result" : 5 3 | } 4 | -------------------------------------------------------------------------------- /executorWdl/src/test/resources/task_runner/two_files_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "file1": "dx://dxCompiler_playground:/test_data/fileC", 3 | "file2": "dx://dxCompiler_playground:/test_data/1/fileC" 4 | } -------------------------------------------------------------------------------- /project/build.properties: -------------------------------------------------------------------------------- 1 | sbt.version=1.6.1 2 | -------------------------------------------------------------------------------- /scripts/Makefile: -------------------------------------------------------------------------------- 1 | # create the copy_file applet 2 | app: 3 | dx build --app --publish dxwdl_copy 4 | -------------------------------------------------------------------------------- /scripts/docker_image/docker.env: -------------------------------------------------------------------------------- 1 | # Specify the dxCompiler version from 2 | # https://github.com/dnanexus/dxCompiler/releases 3 | VERSION=2.11.6 4 | -------------------------------------------------------------------------------- /scripts/dxcompiler_copy/README.md: -------------------------------------------------------------------------------- 1 | # dxCompiler Copy File 2 | 3 | Copy a file to a different geographic region. 4 | -------------------------------------------------------------------------------- /scripts/requirements.txt: -------------------------------------------------------------------------------- 1 | # requirements of the build scripts 2 | dxpy 3 | pyyaml 4 | termcolor 5 | cryptography>=38.0.3 # not directly required, pinned by Snyk to avoid a vulnerability -------------------------------------------------------------------------------- /test/.gitignore: -------------------------------------------------------------------------------- 1 | X_* 2 | X.* 3 | scratch/ -------------------------------------------------------------------------------- /test/applets/README.md: -------------------------------------------------------------------------------- 1 | # DNAx applets 2 | 3 | A directory with simple dx:applets for testing of FFI calls. 4 | -------------------------------------------------------------------------------- /test/bugs/APPS-824/scatter_over_files_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "test.file_input": ["dx://file-Fq5k02j0ffP5JXfB3bKx4PXg","dx://file-Fq5k02Q0ffP3x8213f9vb0yV","dx://file-G5YG20Q07pb1QbF32K9190jV"] 3 | } -------------------------------------------------------------------------------- /test/bugs/apps_1014.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | task apps_1014 { 4 | command <<< 5 | exit 1 6 | >>> 7 | } -------------------------------------------------------------------------------- /test/bugs/apps_1052_optional_block_inputs_wdl10_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_block_inputs_wdl10.filesCount": 3 3 | } 4 | -------------------------------------------------------------------------------- /test/bugs/apps_1052_optional_block_inputs_wdl11_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_block_inputs_wdl11.filesCount": 3 3 | } 4 | -------------------------------------------------------------------------------- /test/bugs/apps_1052_optional_compound_input_wdl10_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_1052_optional_compound_input_wdl10.t1" : {"inner": {}} 3 | } 4 | -------------------------------------------------------------------------------- /test/bugs/apps_378_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_378.sample_names_out": ["a"], 3 | "apps_378.sample_types_out": ["foo"] 4 | } -------------------------------------------------------------------------------- /test/bugs/apps_573_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_573.out": "1^I1$\n2\\t2$\n3\\^I3$\n4\\\\t4$" 3 | } -------------------------------------------------------------------------------- /test/bugs/apps_579_boolean_flag_expr_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_579_boolean_wf.result" : "x" 3 | } 4 | -------------------------------------------------------------------------------- /test/bugs/apps_579_string_substitution_expr_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_579_sub_wf.result" : "aa" 3 | } 4 | -------------------------------------------------------------------------------- /test/bugs/apps_864_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_864.sample" : "wgs_bam_NA12878_20k_b37_NA12878_20k", 3 | "apps_864.old_fastq_folder" : "test_data/fastq_gz_files", 4 | "apps_864.R1_or_R2" : ".b37" 5 | } -------------------------------------------------------------------------------- /test/bugs/apps_936_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_936.foo": { 3 | "docker_image": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-G66qpGj0yzZq02K9313pJg5G" 4 | } 5 | } -------------------------------------------------------------------------------- /test/bugs/diskspace_exhauster_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "diskspace_exhauster.count": 64 3 | } -------------------------------------------------------------------------------- /test/bugs/nested_pairs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_pairs.messages": ["hello goodbye", "up down"], 3 | "nested_pairs.names": ["a", "b"] 4 | } -------------------------------------------------------------------------------- /test/bugs/write_lines_bug_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "write_lines_bug.files": [ 3 | "dx://dxCompiler_playground:/test_data/fileA", 4 | "dx://dxCompiler_playground:/test_data/fileB" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/bugs/write_lines_bug_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "write_lines_bug.strings": [ 3 | "/home/dnanexus/inputs/input0/fileA", 4 | "/home/dnanexus/inputs/input0/fileB" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cromwell/afters/afters.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "readFromCache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/aliased_subworkflows/subworkflow_wt_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subwf_wt.is" : [1,2,3,4,5,6,7,8,9] 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/cacheBetweenWF/cacheBetweenWF.options: -------------------------------------------------------------------------------- 1 | { 2 | "write_to_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_empty_hint.options: -------------------------------------------------------------------------------- 1 | { 2 | "call_cache_hit_path_prefixes": [] 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_empty_hint_input.json: -------------------------------------------------------------------------------- 1 | { "call_cache_hit_prefixes.yo.salutation": "empty hint" } 2 | -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_no_hint_input.json: -------------------------------------------------------------------------------- 1 | { "call_cache_hit_prefixes.yo.salutation": "no hint" } 2 | -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_cache_hit_prefixes.sup": "sup two roots empty hint miss?" 3 | } -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_two_roots_empty_hint_hit_papi_input.json: -------------------------------------------------------------------------------- 1 | { "call_cache_hit_prefixes.yo.salutation": "two roots empty hint hit" } 2 | -------------------------------------------------------------------------------- /test/cromwell/call_cache_hit_prefixes/call_cache_hit_prefixes_two_roots_empty_hint_miss_papi_input.json: -------------------------------------------------------------------------------- 1 | { "call_cache_hit_prefixes.yo.salutation": "two roots empty hint miss" } 2 | -------------------------------------------------------------------------------- /test/cromwell/checkpointing/checkpointing_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "checkpointing.preempted": "GOTPREEMPTED" 3 | } -------------------------------------------------------------------------------- /test/cromwell/conditionals_tests/nested_lookups/nested_lookups.inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_lookups.needs_wf_input.i": 2050 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/conditionals_tests/simple_if/simple_if_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_if.runMeTrue.s": "done", 3 | "simple_if.runMeFalse.s": null 4 | } -------------------------------------------------------------------------------- /test/cromwell/conditionals_tests/simple_if_workflow_outputs/simple_if_workflow_outputs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_if.rmf": null, 3 | "simple_if.rmt": "done" 4 | } -------------------------------------------------------------------------------- /test/cromwell/confirm_preemptible/confirm_preemptible_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "confirm_preemptible.should_be_false": "FALSE", 3 | "confirm_preemptible.should_be_true": "TRUE" 4 | } -------------------------------------------------------------------------------- /test/cromwell/cromwell_restart_papi_upgrade/cromwell_restart_papi_upgrade.options: -------------------------------------------------------------------------------- 1 | { 2 | "backend": "Papiv2" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/custom_entrypoint/custom_entrypoint_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "custom_entrypoint_wf.hello": "hello world" 3 | } -------------------------------------------------------------------------------- /test/cromwell/custom_mount_point/custom_mount_point.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/declarations/declarations_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "two_step.cgrep.pattern": "first", 3 | "two_step.cgrep.str_decl": "foobar", 4 | "two_step.flags_suffix": "s" 5 | } 6 | 7 | -------------------------------------------------------------------------------- /test/cromwell/default_runtime_attributes/default_runtime_attributes.options: -------------------------------------------------------------------------------- 1 | { 2 | "default_runtime_attributes": { 3 | "docker": "ubuntu:latest", 4 | "continueOnReturnCode": 1 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /test/cromwell/default_runtime_attributes/default_runtime_attributes_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_default_runtime_attributes.default_runtime_attributes.ohno": "OH NO!" 3 | } -------------------------------------------------------------------------------- /test/cromwell/delete_intermediates/delete_intermediates.options: -------------------------------------------------------------------------------- 1 | { 2 | "delete_intermediate_output_files": true 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/delete_intermediates/no_task_no_output_delete.wdl: -------------------------------------------------------------------------------- 1 | workflow no_task_no_output_delete { 2 | output { 3 | Int notUsed = 0 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/cromwell/docker_alpine/docker_alpine.options: -------------------------------------------------------------------------------- 1 | { 2 | "final_workflow_outputs_dir": "/tmp/outputs" 3 | } -------------------------------------------------------------------------------- /test/cromwell/docker_hash/docker_hash.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_false.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "use_docker_image_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_false_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "docker_image_cache_false_test.is_docker_image_cache_disk_mounted": false 3 | } -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_true.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "use_docker_image_cache": true 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_true_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "docker_image_cache_true_test.is_docker_image_cache_disk_mounted": true 3 | } -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_unspecified.options.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cromwell/docker_image_cache/docker_image_cache_unspecified_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "docker_image_cache_unspecified_test.is_docker_image_cache_disk_mounted": false 3 | } -------------------------------------------------------------------------------- /test/cromwell/empty_string/empty_string_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_hello.goodbye.empty": "" 3 | } -------------------------------------------------------------------------------- /test/cromwell/floating_tags/floating_tags.options: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cromwell/forkjoin/forkjoin_input.json: -------------------------------------------------------------------------------- 1 | { 2 | } -------------------------------------------------------------------------------- /test/cromwell/hello_private_repo/hello_private_repo.inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "hello_private_repo.addressee": "m'Lord" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/http_inputs/http_inputs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "http_inputs.sum.jamie": "https://raw.githubusercontent.com/broadinstitute/cromwell/develop/docs/jamie_the_cromwell_pig.png", 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/input_localization/input_localization.options: -------------------------------------------------------------------------------- 1 | { 2 | "backend": "Local" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/labels/invalid.labels: -------------------------------------------------------------------------------- 1 | { 2 | "": "not a great label key" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/labels/valid.labels: -------------------------------------------------------------------------------- 1 | { 2 | "label-key-1":"label-value-1", 3 | "label-key-2":"label-value-2", 4 | "only-key": "", 5 | "fc-id": "0123-abcd-4567-efgh" 6 | } 7 | -------------------------------------------------------------------------------- /test/cromwell/large_final_workflow_outputs_dir/large_final_workflow_outputs_dir.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "final_workflow_outputs_dir": "gs://cloud-cromwell-dev-self-cleaning-fast" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/length/length_slurm_no_docker.options: -------------------------------------------------------------------------------- 1 | { 2 | "backend": "SlurmNoDocker" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/local_backend/local_backend.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false, 3 | "backend": "Local" 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/local_backend/local_backend_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "local_backend.goodbye.addressee": "m'Lord" 3 | } 4 | 5 | -------------------------------------------------------------------------------- /test/cromwell/lots_of_inputs/lots_of_inputs_input.json: -------------------------------------------------------------------------------- 1 | { "lots_of_inputs.how_many_is_lots": 400 } 2 | -------------------------------------------------------------------------------- /test/cromwell/lots_of_inputs/lots_of_inputs_papiv2_input.json: -------------------------------------------------------------------------------- 1 | { "lots_of_inputs.how_many_is_lots": 10000 } 2 | -------------------------------------------------------------------------------- /test/cromwell/monitoring_image_script/monitoring_image_script_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "monitoring_image_script.monitoring_script_created": "I am the Lizard Queen!" 3 | } -------------------------------------------------------------------------------- /test/cromwell/monitoring_log/monitoring_log.options: -------------------------------------------------------------------------------- 1 | { 2 | "monitoring_script": "gs://cloud-cromwell-dev/some/rounding_script_int.sh" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/multiline_command_line/multiline_command_line_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf.blah.ab": "ab" 3 | } -------------------------------------------------------------------------------- /test/cromwell/non_root_specified_user/non_root_specified_user_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "woot.nobodyUser": "nobody" 3 | } -------------------------------------------------------------------------------- /test/cromwell/optional_declarations/optional_declarations_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "optional_declarations.wf_int": 1, 3 | "optional_declarations.wf_string": "2" 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/papi_cpu_platform/papi_cpu_platform_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cpus.broadwell.cpuPlatform": "Intel Broadwell", 3 | "cpus.haswell.cpuPlatform": "Intel Haswell" 4 | } -------------------------------------------------------------------------------- /test/cromwell/parallel_composite_uploads/caching_off.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/parallel_composite_uploads/parallel_composite_uploads_off.options: -------------------------------------------------------------------------------- 1 | { 2 | "parallel_composite_upload_threshold": "0", 3 | "read_from_cache": false 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/parallel_composite_uploads/parallel_composite_uploads_on.options: -------------------------------------------------------------------------------- 1 | { 2 | "parallel_composite_upload_threshold": "150M", 3 | "read_from_cache": false 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/passingfiles/passingfiles_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "filepassing.consumeFile.contentsAlt": "small file contents", 3 | "filepassing.consumeFile.contents": "small file contents" 4 | } -------------------------------------------------------------------------------- /test/cromwell/prefix/prefix.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/readFromCacheFalse/readFromCache.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/recursive_imports_no_subwf/recimp_nosubwf_outer.wdl: -------------------------------------------------------------------------------- 1 | import "recimp_nosubwf_inner.wdl" as inner 2 | 3 | # Nothing at all 4 | task rins_outer { 5 | command {} 6 | output {} 7 | } 8 | -------------------------------------------------------------------------------- /test/cromwell/reference_disk/reference_disk_test_false.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false, 3 | "use_reference_disks": false 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/reference_disk/reference_disk_test_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_reference_disk_test.is_input_file_a_symlink": false 3 | } -------------------------------------------------------------------------------- /test/cromwell/reference_disk/reference_disk_test_true.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false, 3 | "use_reference_disks": true 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/reference_disk/reference_disk_test_unspecified.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/relative_output_paths/options.json: -------------------------------------------------------------------------------- 1 | { 2 | "final_workflow_outputs_dir": "/tmp/outputs/relative_output_paths", 3 | "use_relative_output_paths": true 4 | } -------------------------------------------------------------------------------- /test/cromwell/requester_pays_gcs/engine_functions.options: -------------------------------------------------------------------------------- 1 | { 2 | "jes_gcs_root": "gs://cromwell_bucket_with_requester_pays/cromwell-execution", 3 | "backend": "Papiv2RequesterPays" 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/requester_pays_gcs/engine_functions_negative.options: -------------------------------------------------------------------------------- 1 | { 2 | "jes_gcs_root": "gs://cromwell_bucket_with_requester_pays/cromwell-execution" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/requester_pays_gcs/localization.options: -------------------------------------------------------------------------------- 1 | { 2 | "backend": "Papiv2RequesterPays" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/runtime_attribute_expressions/runtime_attribute_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "runtime_attribute_expressions.out": "Hello World" 3 | } -------------------------------------------------------------------------------- /test/cromwell/scatter_simples/nocallcache.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/single_to_array_conversion/single_to_array_conversion_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "oneToMany.listFiles.result": "hello" 3 | } -------------------------------------------------------------------------------- /test/cromwell/ssh_access/ssh_access.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "enable_ssh_access": true 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/string_interpolation/string_interpolation_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_wf.echo.greeting": "world", 3 | "echo_wf.echo.out": "foobar" 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/string_interpolation_optional/string_interpolation_optional_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_wf.string_interpolation_task.out": "" 3 | } -------------------------------------------------------------------------------- /test/cromwell/sub_sub/sub.wdl: -------------------------------------------------------------------------------- 1 | import "sub_sub.wdl" as sub_sub 2 | 3 | workflow wf { 4 | scatter (i in range(2)) { 5 | call sub_sub.wf 6 | } 7 | } 8 | -------------------------------------------------------------------------------- /test/cromwell/sub_sub/sub_sub.wdl: -------------------------------------------------------------------------------- 1 | import "sub_sub_sub.wdl" as sub_sub_sub 2 | 3 | workflow wf { 4 | scatter (i in range(2)) { 5 | call sub_sub_sub.wf 6 | } 7 | } 8 | -------------------------------------------------------------------------------- /test/cromwell/sub_sub/top.wdl: -------------------------------------------------------------------------------- 1 | import "sub.wdl" as sub 2 | 3 | workflow wf { 4 | scatter (i in range(2)) { 5 | call sub.wf 6 | } 7 | } 8 | -------------------------------------------------------------------------------- /test/cromwell/sub_workflow_hello_world/sub_workflow_hello_world_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "main_workflow.main_output": "Hello sub world!" 3 | } -------------------------------------------------------------------------------- /test/cromwell/symlink_localization/symlink_localization.options: -------------------------------------------------------------------------------- 1 | { 2 | "backend": "Local" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell/virtual_private_cloud/wf_zone_options.json: -------------------------------------------------------------------------------- 1 | { 2 | "default_runtime_attributes": { 3 | "zones": "us-east1-c" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/cromwell/volatile_disables_cache/volatile_disables_cache.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": true, 3 | "write_to_cache": true 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell/workflow_engine_functions/workflow_engine_functions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "w.qux": "qux", 3 | "w.hello": "hello", 4 | "w.world": "world", 5 | "w.bar": "bar" 6 | } -------------------------------------------------------------------------------- /test/cromwell/writeToCache/writeToCache.options: -------------------------------------------------------------------------------- 1 | { 2 | "write_to_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/abort/scheduled_abort.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/attempt_to_localize_bucket_as_file/bucket_name_with_no_trailing_slash.json: -------------------------------------------------------------------------------- 1 | { 2 | "localizer_workflow.input_file": "gs://gcp-public-data-landsat" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/attempt_to_localize_bucket_as_file/bucket_name_with_trailing_slash.json: -------------------------------------------------------------------------------- 1 | { 2 | "localizer_workflow.input_file": "gs://gcp-public-data-landsat/" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/cont_while_possible/cont_while_possible.options: -------------------------------------------------------------------------------- 1 | { 2 | "workflow_failure_mode": "ContinueWhilePossible" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/empty_filename/oops.inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_filename.file": "" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/failures/invalid_wdl/invalid_wdl.wdl: -------------------------------------------------------------------------------- 1 | task blahblah }{ 2 | 3 | workflow notgonna{work}flow {} 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/failures/restart_while_failing/restart_while_failing.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/import_passwd/import_passwd.wdl: -------------------------------------------------------------------------------- 1 | import "/etc/passwd" as whoa_there_buddy 2 | 3 | workflow foo { 4 | call whoa_there_buddy.dont_do_that 5 | } 6 | -------------------------------------------------------------------------------- /test/cromwell_failed/import_passwd_url/import_passwd_url.wdl: -------------------------------------------------------------------------------- 1 | import "file:///etc/passwd" as whoa_there_buddy 2 | 3 | workflow foo { 4 | call whoa_there_buddy.dont_do_that 5 | } 6 | -------------------------------------------------------------------------------- /test/cromwell_failed/invalid_inputs_json/invalid_inputs_json_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "intentionally_missing_the_close_brace": "oh the humanity" 3 | -------------------------------------------------------------------------------- /test/cromwell_failed/invalid_inputs_json/invalid_inputs_json_object_input.json: -------------------------------------------------------------------------------- 1 | this_is_not_a_valid_json_object 2 | -------------------------------------------------------------------------------- /test/cromwell_failed/invalid_use_reference_disks_specification/invalid_use_reference_disks_specification.options.json: -------------------------------------------------------------------------------- 1 | { 2 | "use_reference_disks": "I like turtles" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/labels_bad_workflow/badWorkflow_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "hello.foo": "bar" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/max_retries/max_retries.options: -------------------------------------------------------------------------------- 1 | { 2 | "default_runtime_attributes": { 3 | "maxRetries": 1 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/cromwell_failed/missing_input_failure/missing_input_failure_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_input_failure.wf_hello_input": "gs://nonexistingbucket/path/doesnt/exist" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/missing_sub_inputs/missing_sub_inputs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_sub_inputs.x": "gs://cloud-cromwell-dev/log.txt" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/monitoring_script_localization_failure/monitoring_script_localization_failure.options: -------------------------------------------------------------------------------- 1 | { 2 | "monitoring_script": "gs://cloud-cromwell-dev/nonexistent_monitoring_script.sh" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/no_new_calls/no_new_calls.options: -------------------------------------------------------------------------------- 1 | { 2 | "read_from_cache": false, 3 | "workflowFailureMode": "NoNewCalls" 4 | } 5 | -------------------------------------------------------------------------------- /test/cromwell_failed/read_file_limits/read_file_limits.options: -------------------------------------------------------------------------------- 1 | { 2 | "workflow_failure_mode": "ContinueWhilePossible" 3 | } 4 | -------------------------------------------------------------------------------- /test/cromwell_failed/retry_with_more_memory/retry_with_more_memory.options: -------------------------------------------------------------------------------- 1 | { 2 | "memory_retry_multiplier" : 1.1 3 | } 4 | -------------------------------------------------------------------------------- /test/custom_reorg/test_reorg_no_config_extras.json: -------------------------------------------------------------------------------- 1 | { 2 | "custom_reorg": { 3 | "app_id": "applet-Fg623fj0jy8q7jjv9xV6q5fQ", 4 | "conf": null 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /test/cwl/cat_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.file": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-FGzzpkQ0ffPJX74548Vp6670" 3 | } -------------------------------------------------------------------------------- /test/cwl/cat_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat.contents": "It is going to get a lot cooler next year." 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/anon_enum_inside_array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "anon_enum_inside_array.first": { 3 | "species": "mus_musculus" 4 | }, 5 | "anon_enum_inside_array.second": "homo_sapiens" 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/bool-empty-inputbinding_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "bool-empty-inputbinding.args": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat1-testcli_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat1-testcli.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat1-testcli_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat1-testcli.args": ["cat", "hello.txt"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat1-testcli_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat1-testcli.args": ["cat", "-n", "hello.txt"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat3-nodocker_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat3-nodocker.file1": { 3 | "class": "File", 4 | "contents": "Hello file literal" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat3-tool_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat3-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat3-tool_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat3-tool.file1": { 3 | "class": "File", 4 | "contents": "Hello file literal" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat4-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat4-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cat5-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cat5-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cores_float_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cwl/hello.txt: -------------------------------------------------------------------------------- 1 | Hello world! 2 | -------------------------------------------------------------------------------- /test/cwl_conformance/tools/cwl/literal.txt: -------------------------------------------------------------------------------- 1 | I'm a File literal; howdy! 2 | -------------------------------------------------------------------------------- /test/cwl_conformance/tools/default_path_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/dir2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir2.indir": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/testdir/" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/dir3_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir3.inf": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.tar" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/dir5_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir5.indir": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/testdir/" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/dir6_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir6.indir": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/testdir/" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/dir_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dir.indir": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/testdir/" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/docker-output-dir_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/docker-run-cmd_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-position-expr_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-position-expr.one": 1, 3 | "echo-position-expr.two": 2 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-position-expr_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-position-expr.out": "🕺 1 singular sensation!\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool-packed2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool-packed2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool-packed2.out": "hello test env\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool-packed_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool-packed_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool-packed.out": "hello test env\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool.in": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool.in": null 3 | } 4 | -------------------------------------------------------------------------------- /test/cwl_conformance/tools/echo-tool_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-tool.out": "hello test env\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/empty-array-input_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty-array-input.array": [], 3 | "empty-array-input.args___py": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ85b9j0yzZxbQ1Z1V5z98qZ" 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/empty-array-input_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty-array-input.args": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/env-tool1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "env-tool1.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/envvar2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/envvar2_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/envvar3_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/envvar_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/envvar_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/exit-success_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/exit-success_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/exitcode_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "exitcode.code": 7 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/glob-expr-list_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "glob-expr-list.ids": [ 3 | "a", 4 | "b", 5 | "c" 6 | ] 7 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/glob-path-error_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/glob_directory_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/glob_test_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/imported-hint_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/initialwork-path_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/inline-js_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "inline-js.args___py": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ85b9j0yzZxbQ1Z1V5z98qZ" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/io-file-or-files_input4.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-file-or-files.input": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/iwdr-entry_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "iwdr-entry.message": "hello" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/linkfile_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "linkfile.src": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ8G8580yzZzVKY57VqG1kbb" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_deep1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_deep1.d": { 3 | "class": "Directory", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/tmp1/" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_deep1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_deep1.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_deep2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_deep2.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_none1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_none1.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_none2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_none2.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_none3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_none3.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_shallow1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_shallow1.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/listing_shallow2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "listing_shallow2.out": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/loadContents-limit_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "loadContents-limit.filelist": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ86Bf00yzZj1kGB1VF6bJBv" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/loadContents-limit_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/metadata_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "metadata.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/hello.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/metadata_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/nameroot_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "nameroot.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/whale.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/nested-array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested-array.letters": [ 3 | [ 4 | "a" 5 | ] 6 | ] 7 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/networkaccess2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/networkaccess_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/networkaccess_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/no-outputs-tool_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-defined_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-defined_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-defined.out": "t\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-defined_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-defined.out": "f\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-expression2-tool_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-expression2-tool_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-expression2-tool.i1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-expression2-tool_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-expression2-tool.i1": "null" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/null-expression2-tool_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-expression2-tool.output": 2 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/optional-numerical-output-0_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "optional-numerical-output-0.out": 0 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/output-arrays-int_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "output-arrays-int.i": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/output-arrays-int_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "output-arrays-int.o": [0, 1, 2] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/params2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/params_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/parseInt-tool_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "parseInt-tool.output": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/record-in-secondaryFiles_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/record-out-secondaryFiles_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/record-sd-secondaryFiles_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/runtime-paths-distinct_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/schemadef-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "schemadef-tool.hello": { 3 | "a": "hello", 4 | "b": "world" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/shellchar2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/shellchar_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stage-unprovided-file_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "stage-unprovided-file.args___py": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ85b9j0yzZxbQ1Z1V5z98qZ" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stage-unprovided-file_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "stage-unprovided-file.args": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stagefile_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "stagefile.infile": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/whale.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stderr-mediumcut_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stderr-shortcut_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stderr_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/storage_float_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/symlink-illegal_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/symlink-legal_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/test-cwl-out2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/test-cwl-out_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/test/special_file: -------------------------------------------------------------------------------- 1 | 42 -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit3_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit3_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit4_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit5_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "timelimit5.status": "Done" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/timelimit_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/valueFrom-constant_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "valueFrom-constant.args": [ 3 | "replacementValue" 4 | ] 5 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/vf-concat_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/vf-concat_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ87YJ00yzZq4KJ51KF966fB" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/vf-concat_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "vf-concat.out": "\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/vf-concat_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "vf-concat.out": "a string\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/wc2-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc2-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ87YJ00yzZq4KJ51KF966fB" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/wc2-tool_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc2-tool.output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/wc4-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc4-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ87YJ00yzZq4KJ51KF966fB" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/wc4-tool_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc4-tool.output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/tools/writable-dir-docker_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/writable-dir_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001_nojs.test": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001_nojs.test": false 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001_nojs.out1": "foo 23" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_nojs_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001_nojs.out1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001.out1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-001_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-001.out1": "foo 3" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-002_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-002.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-002_nojs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-002_nojs.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-002_nojs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-002_nojs.out1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-002_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-002.out1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.val": 0 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1_nojs.test1": true, 3 | "cond-wf-003-1_nojs.test2": false 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1_nojs.test1": false, 3 | "cond-wf-003-1_nojs.test2": false 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_nojs_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1_nojs.test1": false, 3 | "cond-wf-003-1_nojs.test2": true 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1_nojs.out1": "foo 23" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_nojs_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1_nojs.out1": "foo 23" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.out1": "foo 0" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.out1": "foo 3" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003-1_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003-1.out1": "foo 3" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003_nojs.test": false 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003_nojs.test": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003_nojs.out1": "Direct" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_nojs_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003_nojs.out1": "foo 23" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003.out1": "Direct" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-003_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-003.out1": "foo 3" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004_nojs.test": false 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004_nojs.test": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004_nojs.out1": "Direct" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-004_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-004.out1": "Direct" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-005_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-005.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-005_nojs_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-005_nojs.test": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006_nojs.test1": false, 3 | "cond-wf-006_nojs.test2": true 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006_nojs.test1": true, 3 | "cond-wf-006_nojs.test2": true 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006_nojs.out1": "bar 23" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-006_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-006.out1": "bar 1" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.val": 0 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.val": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.test1": false, 3 | "cond-wf-007_nojs.test2": false 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.test1": false, 3 | "cond-wf-007_nojs.test2": true 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.test1": true, 3 | "cond-wf-007_nojs.test2": true 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.out1": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.out1": [ 3 | "bar 23" 4 | ] 5 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_nojs_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.out1": [ 3 | "foo 23", 4 | "bar 23" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.out1": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.out1": [ 3 | "bar 1" 4 | ] 5 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.out1": [ 3 | "foo 3", 4 | "bar 3" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009.data": [ 3 | 1, 4 | 2, 5 | 3, 6 | 4, 7 | 5, 8 | 6 9 | ], 10 | "cond-wf-009.val": 2 11 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009.data": [ 3 | 1, 4 | 2, 5 | 3, 6 | 4, 7 | 5, 8 | 6 9 | ], 10 | "cond-wf-009.val": 4 11 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_nojs_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009_nojs.test": false 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_nojs_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009_nojs.test": true 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_nojs_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009_nojs.out1": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-009_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-009.out1": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-010_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-010.val": [ 3 | 1, 4 | 2, 5 | 3, 6 | 4, 7 | 5, 8 | 6 9 | ] 10 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-010_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-010_nojs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-010_nojs.out1": [ 3 | "foo 4", 4 | "foo 5", 5 | "foo 6" 6 | ] 7 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-010_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-010.out1": [ 3 | "foo 4", 4 | "foo 5", 5 | "foo 6" 6 | ] 7 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-011_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-012_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-012.val": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-012_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-013_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-013.in1": [ 3 | 1, 4 | 2, 5 | 3, 6 | 4, 7 | 5, 8 | 6 9 | ] 10 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-013_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/conflict-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "collision.input_1" : "Hello World", 3 | "collision.input_2" : "How are you?" 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines1-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines1-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines10-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines10-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-extra-step-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-extra-step-wf.count_output": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-null-step-wf-noET_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-null-step-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-null-step-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-null-step-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-wf_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-wf_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-wf.file1": null 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-wf_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-wf_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines11-wf_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines11-wf.count_output": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines12-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines12-wf.count_output": 34 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines13-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines13-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines14-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines14-wf.count_output": [ 3 | 16, 4 | 1 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines15-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines15-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines16-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines16-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines17-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines17-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines18-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines18-wf.count_output": [ 3 | 16, 4 | 1 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines19-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines19-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines2-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines2-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines3-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines3-wf.count_output": [ 3 | 16, 4 | 1 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines4-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines4-wf.count_output": [ 3 | 16, 4 | 1 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines5-wf_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines5-wf_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines5-wf.count_output": 1 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines5-wf_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines5-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines6-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines6-wf.count_output": [ 3 | 32, 4 | 2 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines7-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines7-wf.count_output": 34 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines8-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines8-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines9-wf-noET_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines9-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/count-lines9-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "count-lines9-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/dynresreq-workflow-inputdefault_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/dynresreq-workflow-stepdefault_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/dynresreq-workflow-tooldefault_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/echo-wf-default_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/echo-wf-default_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo-wf-default.default_output": "workflow_default" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/env-wf1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "env-wf1.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/env-wf2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "env-wf2.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/env-wf3_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "env-wf3.in": "hello test env" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/fail-unconnected_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/import_schema-def_packed_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.bam": "a.bam", 3 | "main.capture_kit": { 4 | "bait": "abait" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.bar": 7 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.bar": "7" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_input4.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.bar": [ 3 | 1, 4 | "moocow" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_input5.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.bar": { 3 | "moo": 1, 4 | "cow": 5 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.t1": 7 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.t1": "7" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.t1": "File" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_results4.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.t1": [ 3 | 1, 4 | "moocow" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-any-wf-1_results5.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-any-wf-1.t1": { 3 | "moo": 1, 4 | "cow": 5 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-file-default-wf_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-tool-and-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-tool-and-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-default-tool-and-wf.o": 13 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-wf_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-default-wf.i": 5 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-wf_input2.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-wf_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-default-wf.o": 10 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-default-wf_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-default-wf.o": 8 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-optional-wf_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-optional-wf.i": 5 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-optional-wf_input2.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-optional-wf_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-optional-wf.o": 10 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-optional-wf_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-optional-wf.o": 4 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-wf.i": 5 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-int-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-int-wf.o": 10 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-union-input-default-wf_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-union-input-default-wf_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-union-input-default-wf.o": "the default value" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/io-union-input-default-wf_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "io-union-input-default-wf.o": "File" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/no-outputs-wf_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/output-arrays-int-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "output-arrays-int-wf.i": 3 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/output-arrays-int-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "output-arrays-int-wf.o": 12 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/parseInt-tool_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "parseInt-tool.output": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/pass-unconnected_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/pass-unconnected_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "pass-unconnected.out": "hello inp1\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/revsort-packed_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.input": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/whale.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/revsort_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "revsort.input": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/whale.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-valuefrom-wf4_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-valuefrom-wf4.out": ["foo one one three", "foo one two four"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-valuefrom-wf6_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-valuefrom-wf6.scattered_messages": [ 3 | "message a", 4 | "message b" 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf1.inp": ["one", "two", "three", "four"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf1.out": ["foo one", "foo two", "foo three", "foo four"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf2_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf2.inp1": [ 3 | "one", 4 | "two" 5 | ], 6 | "scatter-wf2.inp2": [] 7 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf2_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf2.out": [ 3 | [], 4 | [] 5 | ] 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.inp1": ["one", "two"], 3 | "main.inp2": ["three", "four"] 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.inp1": [], 3 | "main.inp2": ["one", "two"] 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_input3.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.inp1": ["one", "two"], 3 | "main.inp2": [] 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf3.out": ["foo one three", "foo one four", "foo two three", "foo two four"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf3.out": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf3_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf3.out": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf4_input1.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.inp1": ["one", "two"], 3 | "main.inp2": ["three", "four"] 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf4_input2.json: -------------------------------------------------------------------------------- 1 | { 2 | "main.inp1": [], 3 | "main.inp2": [] 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf4_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf4.out": ["foo one three", "foo two four"] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/scatter-wf4_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf4.out": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/schemadef-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "schemadef-tool.hello": { 3 | "a": "hello", 4 | "b": "world" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/schemadef-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "schemadef-wf.hello": { 3 | "a": "hello", 4 | "b": "world" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom-wf.count_output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom2-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom2-wf.a": 1, 3 | "step-valuefrom2-wf.b": 2 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom2-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom2-wf.val": "3\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom3-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom3-wf.a": 1, 3 | "step-valuefrom3-wf.b": 2 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom3-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom3-wf.val": "3\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom4-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom4-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom4-wf.val": "moocow\n" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/step-valuefrom5-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom5-wf.val1": "whale.txt\n", 3 | "step-valuefrom5-wf.val2": "step1_out\n" 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/steplevel-resreq_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/sum-wf-noET_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "sum-wf-noET.int_1": 5, 3 | "sum-wf-noET.int_2": 7 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/sum-wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "sum-wf.int_1": 5, 3 | "sum-wf.int_2": 7 4 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/sum-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "sum-wf.result": 12 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit2-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit2-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "timelimit2-wf.o": "time passed" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit3-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit3-wf_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "timelimit3-wf.o": "time passed" 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit4-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wc2-tool_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc2-tool.file1": { 3 | "class": "File", 4 | "location": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/whale.txt" 5 | } 6 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wc2-tool_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc2-tool.output": 16 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wf-loadContents2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf-loadContents2.my_int": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wf-loadContents3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf-loadContents3.my_int": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wf-loadContents4_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf-loadContents4.my_int": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/wf-loadContents_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf-loadContents.my_int": 42 3 | } -------------------------------------------------------------------------------- /test/cwl_cromwell/InitialWorkDirRequirement/inline_file_custom_entryname_input.yaml: -------------------------------------------------------------------------------- 1 | script_name: "astounding.py" # default value of type "string". 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/InitialWorkDirRequirement/inline_file_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_ad_hoc_file_test/cwl-test_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_ad_hoc_file_test/cwl_ad_hoc_file_test_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_cache_between_workflows/cwl_cache_between_workflows_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_cache_within_workflow/cwl_cache_within_workflow_input.yaml: -------------------------------------------------------------------------------- 1 | radius: 4.029121233 # type "float" 2 | pi: 3.14159 # type "float" 3 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_docker_size/cwl_docker_size_input.txt: -------------------------------------------------------------------------------- 1 | And you people, you're all astronauts, on some kind of star trek. 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_docker_size/cwl_docker_size_input.yaml: -------------------------------------------------------------------------------- 1 | INPUT: 2 | - class: File 3 | path: "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/cwl_docker_size_input.txt" 4 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_dynamic_initial_workdir/cwl_dynamic_initial_workdir_input.yaml: -------------------------------------------------------------------------------- 1 | indir: # type "Directory" 2 | class: Directory 3 | path: testdir 4 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_expressionLib/cwl_expressionLib_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_format/foo.fasta: -------------------------------------------------------------------------------- 1 | >sequence #1 2 | GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT 3 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_format/foo.fastq: -------------------------------------------------------------------------------- 1 | @SEQ_ID 2 | GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT 3 | + 4 | !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 5 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_glob_sort/cwl_glob_sort_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_hello/cwl_hello_input.yaml: -------------------------------------------------------------------------------- 1 | message: Hello m'Lord! # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_import_type/capture_kit.yml: -------------------------------------------------------------------------------- 1 | - name: capture_kit 2 | type: record 3 | fields: 4 | - name: bait 5 | type: string 6 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_import_type/test_wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "bam": "a.bam", 3 | "capture_kit": { 4 | "bait": "abait" 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_import_type/touch_input.yaml: -------------------------------------------------------------------------------- 1 | input: a_string # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_import_type_packed/capture_kit.yml: -------------------------------------------------------------------------------- 1 | - name: capture_kit 2 | type: record 3 | fields: 4 | - name: bait 5 | type: string 6 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_import_type_packed/test_pack_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "bam": "a.bam", 3 | "capture_kit": { 4 | "bait": "abait" 5 | } 6 | } 7 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_input_binding_expression/cwl_input_binding_expression_input.yaml: -------------------------------------------------------------------------------- 1 | hello: hello # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_input_json/cwl_input_json_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_interpolated_strings/cwl_interpolated_strings_input.yaml: -------------------------------------------------------------------------------- 1 | qux: qux # type "string" 2 | bar: bar # type "string" 3 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_optionals/cwl_optionals.json: -------------------------------------------------------------------------------- 1 | {"message": ["foo","bar"]} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_prefix_for_array/prefix_for_array_input.yaml: -------------------------------------------------------------------------------- 1 | bonus: # array of type "string" 2 | - first 3 | - second 4 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_recursive_link_directories/cwl_recursive_link_directories_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_resources/cwl_disk_resources_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_resources/cwl_inputdir_zero_doesnt_localize_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_resources/cwl_resources_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_restart/cwl_restart_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_run/1st-tool_input.yaml: -------------------------------------------------------------------------------- 1 | message: Hello CWL! # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bam.txt: -------------------------------------------------------------------------------- 1 | bam -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bam.txt.also: -------------------------------------------------------------------------------- 1 | bam -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bar.txt: -------------------------------------------------------------------------------- 1 | bar -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bar.txt.also: -------------------------------------------------------------------------------- 1 | bar -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/baz.txt: -------------------------------------------------------------------------------- 1 | baz -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/baz.txt.also: -------------------------------------------------------------------------------- 1 | baz -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bim.txt: -------------------------------------------------------------------------------- 1 | bim -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/bim.txt.also: -------------------------------------------------------------------------------- 1 | bim -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/foo.txt: -------------------------------------------------------------------------------- 1 | foo -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_secondary_files/foo.txt.also: -------------------------------------------------------------------------------- 1 | foo -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_stdout_expression/cwl_stdout_expression_input.yaml: -------------------------------------------------------------------------------- 1 | bar: bar # type "string" 2 | foo: foo # type "string" 3 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_three_step/cwl_three_step_caller_wf_input.yaml: -------------------------------------------------------------------------------- 1 | pin: "v" # default value of type "string". 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_three_step/cwl_three_step_input.yaml: -------------------------------------------------------------------------------- 1 | pattern: v # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwls/cwl_scatter-wf1_input.yaml: -------------------------------------------------------------------------------- 1 | inp2: baz # type "string" 2 | inp: # array of type "string" 3 | - foo 4 | - bar 5 | -------------------------------------------------------------------------------- /test/cwl_selected_wf/opencravat/oc_input.yaml: -------------------------------------------------------------------------------- 1 | input: # type "File" 2 | class: File 3 | path: dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:/test_data/cwl/oc_hg38.vcf -------------------------------------------------------------------------------- /test/docker/biocontainers_extras.json: -------------------------------------------------------------------------------- 1 | { 2 | "default_runtime_attributes" : { 3 | "docker" : "biocontainers/samtools:v1.7.0_cv4" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/docker/broad_genomics_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/docker/dockerhub_test_image/Makefile: -------------------------------------------------------------------------------- 1 | VERSION=1.0 2 | 3 | all: build_homedir 4 | docker build -t orodeh/dxwdl_test:${VERSION} . 5 | docker push orodeh/dxwdl_test:${VERSION} 6 | -------------------------------------------------------------------------------- /test/docker/dynamic_docker_image_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "dynamic_docker_image.docker_dxfile" : "dx:///ubuntu-bionic.tar" 3 | } -------------------------------------------------------------------------------- /test/docker/dynamic_docker_image_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "dynamic_docker_image.cat": "hello world" 3 | } -------------------------------------------------------------------------------- /test/docker/ecr_docker_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "ecr_docker.s": "hello" 3 | } -------------------------------------------------------------------------------- /test/docker/native_docker_file_image_gzip_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "native_docker_file_image_gzip.result" : "bionic" 3 | } 4 | -------------------------------------------------------------------------------- /test/docker/native_docker_file_image_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "native_docker_file_image.result" : "bionic" 3 | } 4 | -------------------------------------------------------------------------------- /test/docker/private_registry_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/docker/private_registry_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "private_registry.result" : "Major Major" 3 | } 4 | -------------------------------------------------------------------------------- /test/docker/samtools_count_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "samtools_count.bam" : "dx://dxCompiler_playground:/test_data/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam" 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/advanced_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "advanced.pattern" : "jar", 3 | "advanced.file" : "dx://dxCompiler_playground:/test_data/fileB", 4 | "advanced.species" : "Arctic fox" 5 | } 6 | -------------------------------------------------------------------------------- /test/draft2/bad_status2_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/bad_status_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/call_with_defaults1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_with_defaults1.x" : 1, 3 | "call_with_defaults1.flag" : true 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/call_with_defaults1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_with_defaults1.result" : 4 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/call_with_defaults2_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/call_with_defaults2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_with_defaults2.r1" : "Hello, world", 3 | "call_with_defaults2.r2" : "Hello, world", 4 | "call_with_defaults2.r3" : "Hello, Sandy" 5 | } 6 | -------------------------------------------------------------------------------- /test/draft2/conditionals2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals2.flag" : true 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/conditionals2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals2.mul": [5, 1, 4], 3 | "conditionals2.add2_r": 5 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/conditionals_base_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/conditionals_base_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "conditionals_base.results" : [1, 100], 3 | "conditionals_base.nea" : [5,7] 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/files_input_cromwell.json: -------------------------------------------------------------------------------- 1 | { 2 | "files.f": "local/X.txt", 3 | "files.f1": "local/Y.txt", 4 | "files.f2": "local/Z.txt" 5 | } 6 | -------------------------------------------------------------------------------- /test/draft2/files_with_the_same_name_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "files_with_the_same_name.result" : 114 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/hello_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/just_fail_wf.wdl: -------------------------------------------------------------------------------- 1 | workflow just_fail_wf { 2 | call just_fail 3 | } 4 | 5 | task just_fail { 6 | command { 7 | exit 1 8 | } 9 | } 10 | -------------------------------------------------------------------------------- /test/draft2/modulo_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "modulo.n": 7 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/modulo_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "modulo.mulr": [0, 2, 4, 6, 1, 3, 5], 3 | "modulo.addr": [3, 4, 5, 6, 0, 1, 2] 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/movies_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "movies.m_name" : "The diving bell and the butterfly" 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/movies_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "movies.stage-0.score": 0.6000000000000001 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/multiple_imports_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/multiple_imports_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "multiple_imports.r_mul" : 40, 3 | "multiple_imports.r_con" : "carrots_coconut" 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/shapes_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "shapes.num" : 3 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/shapes_result.json: -------------------------------------------------------------------------------- 1 | { 2 | "shapes.r1" : [0, 1, 4], 3 | "shapes.r2" : 1000 4 | } 5 | -------------------------------------------------------------------------------- /test/draft2/subblocks2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks2.numbers" : [ 1, 2, 4 ] 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/subblocks2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks2.ms": [4, 5, 7] 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/subblocks_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks.numbers" : [ 1, 2, 4 ] 3 | } 4 | -------------------------------------------------------------------------------- /test/draft2/subblocks_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "subblocks.mul_a": [2, 4, 1], 3 | "subblocks.add_a": [2, 3, 5], 4 | "subblocks.sub_a": [1, 2, 4] 5 | } 6 | -------------------------------------------------------------------------------- /test/draft2/var_type_change_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/draft2/var_type_change_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "var_type_change.result": ["Banana is good to eat", 3 | "Apple is good to eat"] 4 | } 5 | -------------------------------------------------------------------------------- /test/imports/A_inputs.json: -------------------------------------------------------------------------------- 1 | { 2 | "A.x" : 1, 3 | "A.y" : 2 4 | } 5 | -------------------------------------------------------------------------------- /test/input_file/echo_pairs_input.json: -------------------------------------------------------------------------------- 1 | {"echo_pairs.pairs_of_words": 2 | [ 3 | ["alpine", "env"], 4 | ["shasta", "lake"] 5 | ] 6 | } 7 | -------------------------------------------------------------------------------- /test/input_file/echo_pairs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_pairs.all_echoed_words" : [ "alpine env", "shasta lake"] 3 | } 4 | -------------------------------------------------------------------------------- /test/input_file/population_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "population.start" : 0.8, 3 | "next_year.factor" : 3.4 4 | } 5 | -------------------------------------------------------------------------------- /test/input_file/population_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "population.result" : 544 3 | } 4 | -------------------------------------------------------------------------------- /test/local/X.txt: -------------------------------------------------------------------------------- 1 | Pear, Apples, Coconut 2 | -------------------------------------------------------------------------------- /test/local/Y.txt: -------------------------------------------------------------------------------- 1 | Wrench, Nut, Screwdriver 2 | -------------------------------------------------------------------------------- /test/local/Z.txt: -------------------------------------------------------------------------------- 1 | Zebra, Elephant, Mountain Lion 2 | -------------------------------------------------------------------------------- /test/manifest/simple_manifest_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_manifest.input_manifest___": { 3 | "s": "joe", 4 | "f": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-FGzzpkQ0ffPJX74548Vp6670" 5 | } 6 | } -------------------------------------------------------------------------------- /test/manifest/view_and_count_manifest_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "view_and_count.input_manifest___": { 3 | "bam": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-GJ74FPj0yzZvpF8Z4kq03v9V" 4 | } 5 | } -------------------------------------------------------------------------------- /test/nested/apps_1128_frag_native_instance_type_override_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/nested/apps_1177_native_indirect_override_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/nested/apps_1197_native_frag_default_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/nested/apps_612_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_612.b": true, 3 | "apps_612.x": "hello" 4 | } -------------------------------------------------------------------------------- /test/nested/apps_612_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "apps_612.out": "hello" 3 | } -------------------------------------------------------------------------------- /test/nested/four_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.username" : "Alberta" 3 | } 4 | -------------------------------------------------------------------------------- /test/nested/four_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "four_levels.r2": [null, "hello_clease"], 3 | "four_levels.r1": null, 4 | "four_levels.r3": ["john_Alberta", null] 5 | } 6 | -------------------------------------------------------------------------------- /test/nested/nested_optional_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_optional.s": "hello" 3 | } -------------------------------------------------------------------------------- /test/nested/nested_optional_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "nested_optional.outstr": "hello", 3 | "nested_optional.outstr2": "hello" 4 | } -------------------------------------------------------------------------------- /test/nested/param_passing_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "param_passing.num" : 10, 3 | "param_passing.flag" : true 4 | } 5 | -------------------------------------------------------------------------------- /test/nested/param_passing_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "param_passing.r1" : [13, 14, 15], 3 | "param_passing.r2" : 14 4 | } 5 | -------------------------------------------------------------------------------- /test/nested/three_levels_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.score" : 100 3 | } 4 | -------------------------------------------------------------------------------- /test/nested/three_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "three_levels.result1" : 14, 3 | "three_levels.result2" : null 4 | } 5 | -------------------------------------------------------------------------------- /test/nested/two_levels_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/nested/two_levels_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "two_levels.a" : [4, 5, 6], 3 | "two_levels.b" : 4, 4 | "two_levels.c" : 2 5 | } 6 | -------------------------------------------------------------------------------- /test/single_tasks/DiskSpace2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "DiskSpace2.fruits" : "dx://dxCompiler_playground:/test_data/fileB" 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/README.md: -------------------------------------------------------------------------------- 1 | Tests for stand alone tasks. No workflows in this directory. 2 | -------------------------------------------------------------------------------- /test/single_tasks/add3_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "add3.a": 1, 3 | "add3.b": 2, 4 | "add3.c": 4 5 | } 6 | -------------------------------------------------------------------------------- /test/single_tasks/add3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "add3.result" : 7 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/diff2files_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "diff2files.a" : "dx://dxCompiler_playground:/test_data/fileA", 3 | "diff2files.b" : "dx://dxCompiler_playground:/test_data/fileC" 4 | } 5 | -------------------------------------------------------------------------------- /test/single_tasks/diff2files_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "diff2files.result" : 5 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/echo_line_split_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "echo_line_split.results" : "1 hello wdl\n2 hello wdl\n3 hello wdl" 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/empty_stdout_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/single_tasks/empty_stdout_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_stdout.result" : "" 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/find_fastq_in_folder_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "find_fastq_in_folder.fastq_folder" : "/test_data/dont_change/" 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/opt_array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "opt_array.b" : ["dx://dxCompiler_playground:/test_data/fileA", "dx://dxCompiler_playground:/test_data/fileB"] 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/sort_file_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "sort_file.src" : "dx://dxCompiler_playground:/test_data/fileA", 3 | "sort_file.basename" : "happyDays" 4 | } 5 | -------------------------------------------------------------------------------- /test/single_tasks/stream_diff_v1_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "stream_diff_v1.a": "dx://dxCompiler_playground:/test_data/fileB", 3 | "stream_diff_v1.b": "dx://dxCompiler_playground:/test_data/fileC" 4 | } 5 | -------------------------------------------------------------------------------- /test/single_tasks/stream_diff_v1_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "stream_diff_v1.result" : 282 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/symlinks_wc_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "symlinks_wc.a" : "dx://dxCompiler_playground:/test_data/symlinks/1000G_2504_high_coverage.sequence.index" 3 | } 4 | -------------------------------------------------------------------------------- /test/single_tasks/symlinks_wc_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "symlinks_wc.result" : 2528 3 | } 4 | -------------------------------------------------------------------------------- /test/special_flags/add2_extras.json: -------------------------------------------------------------------------------- 1 | { 2 | "ignoreReuse": true 3 | } 4 | -------------------------------------------------------------------------------- /test/special_flags/add2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "add2.a" : 10, 3 | "add2.b" : 11 4 | } 5 | -------------------------------------------------------------------------------- /test/special_flags/add2_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "add2.c" : 21 3 | } 4 | -------------------------------------------------------------------------------- /test/special_flags/add_many_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "add_many.a" : 1, 3 | "add_many.b" : 2, 4 | "add_many.c" : 3, 5 | "add_many.d" : 4 6 | } 7 | -------------------------------------------------------------------------------- /test/special_flags/add_many_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "add_many.result" : 10 3 | } 4 | -------------------------------------------------------------------------------- /test/special_flags/inc_range_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "inc_range.result" : [1, 2, 3] 3 | } 4 | -------------------------------------------------------------------------------- /test/struct/array_structs_input.json: -------------------------------------------------------------------------------- 1 | {"array_structs.words_to_say": [ 2 | {"word": "hello"}, 3 | {"word": "world"} 4 | ]} 5 | -------------------------------------------------------------------------------- /test/struct/array_structs_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "array_structs.out_words" : ["hello", "world"] 3 | } 4 | -------------------------------------------------------------------------------- /test/struct/struct_imported_twice/Block_results.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/180a8848d5319b281f01ce0a458883ca38475f96/test/struct/struct_imported_twice/Block_results.json -------------------------------------------------------------------------------- /test/struct/struct_imported_twice/Blorf_input.json: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/struct/struct_imported_twice/foo_def.wdl: -------------------------------------------------------------------------------- 1 | version 1.0 2 | 3 | struct Foo { 4 | String bar 5 | } 6 | -------------------------------------------------------------------------------- /test/subworkflows/inner_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "inner.lane" : "peach" 3 | } 4 | -------------------------------------------------------------------------------- /test/subworkflows/inner_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "inner.blah" : "peach" 3 | } 4 | -------------------------------------------------------------------------------- /test/subworkflows/outer_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "outer.lane" : "Penny" 3 | } 4 | -------------------------------------------------------------------------------- /test/subworkflows/outer_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "outer.o" : "Penny" 3 | } 4 | -------------------------------------------------------------------------------- /test/subworkflows/trains_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "trains.prefixes" : ["xxx_", "yyy_"], 3 | "trains.ranges" : ["0--1000", "10000--88000"] 4 | } 5 | -------------------------------------------------------------------------------- /test/subworkflows/trains_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "trains.results": ["xxx__0--1000", "xxx__10000--88000", "yyy__0--1000", "yyy__10000--88000"] 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/.gitignore: -------------------------------------------------------------------------------- 1 | dx_extern_one.wdl 2 | dx_extern.wdl -------------------------------------------------------------------------------- /test/wdl_1_0/booleam_param_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "boolean_param.sout2": "false" 3 | } -------------------------------------------------------------------------------- /test/wdl_1_0/call_level2_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_level2.run_name" : "Cherry blossom" 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/call_native_app_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_native_app.my_name" : "Wilbert" 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/call_native_app_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "call_native_app.result" : "hello Wilbert" 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/cast_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "cast.i": 7, 3 | "cast.s": "French horn", 4 | "cast.foo": "dx://dxCompiler_playground:/test_data/fileA" 5 | } 6 | -------------------------------------------------------------------------------- /test/wdl_1_0/cast_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "cast.SumArray_result": 7 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/dict_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "dict.result" : ["carrots", "oranges", "pear", "coconut" ] 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/empty_array_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_array.names": [] 3 | } -------------------------------------------------------------------------------- /test/wdl_1_0/empty_array_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "empty_array.greetings": [], 3 | "empty_array.num_names": 0 4 | } -------------------------------------------------------------------------------- /test/wdl_1_0/environment_passing_deep_nesting_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_passing_deep_nesting.verify" : true 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/environment_passing_deep_nesting_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "environment_passing_deep_nesting.result" : 7 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/instance_types_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "instance_types.i" : 15, 3 | "instance_types.fruits" : "dx://dxCompiler_playground:/test_data/fileB" 4 | } 5 | -------------------------------------------------------------------------------- /test/wdl_1_0/linear_no_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "linear_no_expressions.r1" : 9, 3 | "linear_no_expressions.r2" : 15, 4 | "linear_no_expressions.r3" : 25 5 | } 6 | -------------------------------------------------------------------------------- /test/wdl_1_0/linear_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "linear.result" : 63 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/map_file_key_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "map_file_key.file_key": { 3 | "dx://dxCompiler_playground:/test_data/fileA": "this is string value" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/wdl_1_0/missing_optional_output_file_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "missing_optional_output_file.a" : { 3 | "___": [null, null] 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /test/wdl_1_0/optionals3_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/wdl_1_0/optionals3_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals3.k": [1, 2] 3 | } -------------------------------------------------------------------------------- /test/wdl_1_0/optionals_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals.flag": true 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/optionals_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "optionals.r_mi1": 13, 3 | "optionals.r_mi2": 13, 4 | "optionals.r_mi3": 13, 5 | "optionals.r_mi4": 13 6 | } 7 | -------------------------------------------------------------------------------- /test/wdl_1_0/path_not_taken_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "path_not_taken.equality" : null 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/simple_scatter_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_scatter.num" : 4 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/simple_scatter_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "simple_scatter.result" : [0, 2, 4, 6] 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/streaming_inputs_output.json: -------------------------------------------------------------------------------- 1 | { 2 | "streaming_inputs.r1": "foo", 3 | "streaming_inputs.r2": "bar" 4 | } -------------------------------------------------------------------------------- /test/wdl_1_0/strings_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "strings.result1": "1", 3 | "strings.result2": ["1", "2", "3 INPUT=4", "5", "6 INPUT=7 INPUT=8"], 4 | "strings.result3": "hello buddy" 5 | } 6 | -------------------------------------------------------------------------------- /test/wdl_1_0/top_wf_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "top_wf.arr" : ["Archie"] 3 | } 4 | -------------------------------------------------------------------------------- /test/wdl_1_0/wf_with_input_expressions_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_input_expressions.f": "dx://project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq:file-Fgv1zP00ffP0FVk59X8j9zBX" 3 | } -------------------------------------------------------------------------------- /test/wdl_1_0/wf_with_input_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_input_expressions.x1": "X.txt", 3 | "wf_with_input_expressions.x2": "X.txt" 4 | } -------------------------------------------------------------------------------- /test/wdl_1_0/wf_with_output_expressions_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_output_expressions.a" : 1, 3 | "wf_with_output_expressions.b" : "mensch" 4 | } 5 | -------------------------------------------------------------------------------- /test/wdl_1_0/wf_with_output_expressions_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wf_with_output_expressions.x" : 2, 3 | "wf_with_output_expressions.x2" : "mensch_mensch" 4 | } 5 | -------------------------------------------------------------------------------- /test/wdl_1_1/apps_847_scatter_empty_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_filter.samples_to_exclude": [] 3 | } -------------------------------------------------------------------------------- /test/wdl_1_1/optional_missing_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "test_workflow.database": { 3 | "database_name": "database1", 4 | "num_rows": 5 5 | }, 6 | "test_workflow.prefix": "mystring" 7 | } 8 | -------------------------------------------------------------------------------- /test/wdl_1_1/structs.wdl: -------------------------------------------------------------------------------- 1 | version 1.1 2 | 3 | struct MyStructDB { 4 | String database_name 5 | Int? num_columns 6 | Int num_rows 7 | String? value_types 8 | } 9 | 10 | -------------------------------------------------------------------------------- /test/wdl_1_1/v1_1_dict_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "v1_1_dict.result" : [6, 15] 3 | } 4 | --------------------------------------------------------------------------------