├── .github ├── copilot-instructions.md └── workflows │ ├── build_publish_copy_app.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 ├── 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 │ │ ├── parallel │ │ │ ├── ParallelDef.scala │ │ │ ├── async │ │ │ │ ├── AsyncIterator.scala │ │ │ │ └── AsyncRunnable.scala │ │ │ └── collection │ │ │ │ └── ParIterator.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 │ │ ├── instance_types_results.revert.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 ├── 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 ├── instance_types_results.revert.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 └── 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/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/iwdr-entry_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "iwdr-entry.message": "hello" 3 | } -------------------------------------------------------------------------------- /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_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/metadata_results.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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_results3.json: -------------------------------------------------------------------------------- 1 | { 2 | "null-expression2-tool.output": 2 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/shellchar2_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/shellchar_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/tools/stage-unprovided-file_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "stage-unprovided-file.args": [] 3 | } -------------------------------------------------------------------------------- /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/vf-concat_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "wc2-tool.output": 16 3 | } -------------------------------------------------------------------------------- /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_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_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_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007_nojs.out1": [] 3 | } -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/cond-wf-007_results1.json: -------------------------------------------------------------------------------- 1 | { 2 | "cond-wf-007.out1": [] 3 | } -------------------------------------------------------------------------------- /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_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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_nojs_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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-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-lines5-wf_input1.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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/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/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/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_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-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_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/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_results2.json: -------------------------------------------------------------------------------- 1 | { 2 | "scatter-wf4.out": [] 3 | } -------------------------------------------------------------------------------- /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_results.json: -------------------------------------------------------------------------------- 1 | { 2 | "step-valuefrom2-wf.val": "3\n" 3 | } -------------------------------------------------------------------------------- /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/steplevel-resreq_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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/timelimit3-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /test/cwl_conformance/workflows/timelimit4-wf_input.json: -------------------------------------------------------------------------------- 1 | {} -------------------------------------------------------------------------------- /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_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_expressionLib/cwl_expressionLib_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_format/foo.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/HEAD/test/cwl_cromwell/cwl_format/foo.fasta -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_format/foo.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/HEAD/test/cwl_cromwell/cwl_format/foo.fastq -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_glob_sort/cwl_glob_sort_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_hello/cwl_hello.cwl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dnanexus/dxCompiler/HEAD/test/cwl_cromwell/cwl_hello/cwl_hello.cwl -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_hello/cwl_hello_input.yaml: -------------------------------------------------------------------------------- 1 | message: Hello m'Lord! # type "string" 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_input_json/cwl_input_json_input.yaml: -------------------------------------------------------------------------------- 1 | {} 2 | -------------------------------------------------------------------------------- /test/cwl_cromwell/cwl_optionals/cwl_optionals.json: -------------------------------------------------------------------------------- 1 | {"message": ["foo","bar"]} 2 | -------------------------------------------------------------------------------- /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 | 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-------------------------------------------------------------------------------- /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 -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 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_selected_wf/analysis-workflows/definitions/pipelines/immuno_input.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/cwl_selected_wf/analysis-workflows/definitions/tools/immuno_input.yaml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- 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