From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Thu, 30 Jan 2025 11:15:09 +0100
Subject: Add missing cwl-runner refs

Forwarded: https://github.com/common-workflow-language/cwltool/pull/2095

And mark executable
---
 cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.1/cwl-runner.cwl                         | 0
 cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl                  | 0
 cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl                  | 0
 tests/CometAdapter.cwl                                      | 1 +
 tests/arg-empty-prefix-separate-false.cwl                   | 0
 tests/checker_wf/optional_array_mismatch.cwl                | 1 +
 tests/default_values_list.cwl                               | 0
 tests/echo-badposition-expr.cwl                             | 0
 tests/echo-position-expr.cwl                                | 0
 tests/echo-stdout-log-dir.cwl                               | 0
 tests/env.cwl                                               | 0
 tests/env2.cwl                                              | 0
 tests/env3.cwl                                              | 0
 tests/env4.cwl                                              | 0
 tests/input_deps/docker-array-secondaryfiles.cwl            | 0
 tests/iwdr_bad_expr.cwl                                     | 0
 tests/iwdr_dir_literal_real_file.cwl                        | 0
 tests/load_contents-array.cwl                               | 1 +
 tests/loop-ext/all-output-loop-no-iteration.cwl             | 0
 tests/loop-ext/all-output-loop.cwl                          | 0
 tests/loop-ext/default-value-loop.cwl                       | 0
 tests/loop-ext/invalid-loop-command-line-tool.cwl           | 0
 tests/loop-ext/invalid-loop-expression-tool.cwl             | 0
 tests/loop-ext/invalid-loop-hint.cwl                        | 0
 tests/loop-ext/invalid-loop-scatter.cwl                     | 0
 tests/loop-ext/invalid-loop-when-exception.cwl              | 0
 tests/loop-ext/invalid-loop-when.cwl                        | 0
 tests/loop-ext/invalid-loop-workflow.cwl                    | 0
 tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl | 0
 tests/loop-ext/invalid-no-loopWhen.cwl                      | 0
 tests/loop-ext/invalid-non-boolean-loopWhen.cwl             | 0
 tests/loop-ext/invalid-non-boolean-loopWhen2.cwl            | 0
 tests/loop-ext/invalid-value-from-loop-no-requirement.cwl   | 0
 tests/loop-ext/loop-inside-loop-all.cwl                     | 0
 tests/loop-ext/loop-inside-loop.cwl                         | 0
 tests/loop-ext/loop-inside-scatter.cwl                      | 0
 tests/loop-ext/multi-source-loop.cwl                        | 0
 tests/loop-ext/opt-var-loop.cwl                             | 0
 tests/loop-ext/scatter-inside-loop.cwl                      | 0
 tests/loop-ext/single-var-loop-no-iteration.cwl             | 0
 tests/loop-ext/single-var-loop.cwl                          | 0
 tests/loop-ext/two-vars-loop-2.cwl                          | 0
 tests/loop-ext/two-vars-loop.cwl                            | 0
 tests/loop-ext/value-from-loop.cwl                          | 0
 tests/loop/all-output-loop-no-iteration.cwl                 | 0
 tests/loop/all-output-loop.cwl                              | 0
 tests/loop/default-value-loop.cwl                           | 0
 tests/loop/invalid-loop-scatter.cwl                         | 0
 tests/loop/invalid-loop-when-exception.cwl                  | 0
 tests/loop/invalid-loop-when-exception2.cwl                 | 0
 tests/loop/invalid-multi-source-loop-no-requirement.cwl     | 0
 tests/loop/invalid-no-loopWhen.cwl                          | 0
 tests/loop/invalid-non-boolean-loopWhen.cwl                 | 0
 tests/loop/invalid-non-boolean-loopWhen2.cwl                | 0
 tests/loop/invalid-value-from-loop-no-requirement.cwl       | 0
 tests/loop/loop-inside-loop-all.cwl                         | 0
 tests/loop/loop-inside-loop.cwl                             | 0
 tests/loop/loop-inside-scatter.cwl                          | 0
 tests/loop/multi-source-loop.cwl                            | 0
 tests/loop/opt-var-loop.cwl                                 | 0
 tests/loop/scatter-inside-loop.cwl                          | 0
 tests/loop/single-var-loop-no-iteration.cwl                 | 0
 tests/loop/single-var-loop.cwl                              | 0
 tests/loop/two-vars-loop-2.cwl                              | 0
 tests/loop/two-vars-loop.cwl                                | 0
 tests/loop/value-from-loop.cwl                              | 0
 tests/nested-array.cwl                                      | 1 +
 tests/non_portable.cwl                                      | 0
 tests/non_portable2.cwl                                     | 0
 tests/override/env-tool.cwl                                 | 0
 tests/override/env-tool_v1.1.0-dev1.cwl                     | 0
 tests/override/env-tool_v1.1.cwl                            | 0
 tests/portable.cwl                                          | 0
 tests/reloc/test.cwl                                        | 1 +
 tests/scatter_numbers.cwl                                   | 0
 tests/secondary-files-bad.cwl                               | 0
 tests/secondary-files-required-container.cwl                | 0
 tests/secondary-files-required-missing-container.cwl        | 0
 tests/secondary-files-string-v1.cwl                         | 0
 tests/secondary-files.cwl                                   | 0
 tests/sing_pullfolder_test.cwl                              | 0
 tests/subgraph/1432.cwl                                     | 1 +
 tests/subgraph/env-tool2.cwl                                | 1 +
 tests/subgraph/env-tool2_no_env.cwl                         | 1 +
 tests/subgraph/env-tool2_req.cwl                            | 1 +
 tests/subgraph/env-wf2.cwl                                  | 0
 tests/subgraph/env-wf2_hint_collision.cwl                   | 0
 tests/subgraph/env-wf2_hint_req_collision.cwl               | 0
 tests/subgraph/env-wf2_long.cwl                             | 0
 tests/subgraph/env-wf2_only_hint.cwl                        | 0
 tests/subgraph/env-wf2_req_collision.cwl                    | 0
 tests/subgraph/env-wf2_subwf-packed.cwl                     | 3 ++-
 tests/subgraph/env-wf2_subwf.cwl                            | 0
 tests/subgraph/env-wf2_subwf_b.cwl                          | 0
 tests/subgraph/steplevel-resreq.cwl                         | 0
 tests/subgraph/timelimit2-wf.cwl                            | 0
 tests/test_examples.py                                      | 2 +-
 tests/test_validate.py                                      | 8 ++++----
 tests/trs/Dockstore.cwl                                     | 0
 tests/trs/md5sum-tool.cwl                                   | 0
 tests/trs/md5sum-workflow.cwl                               | 0
 tests/utf_doc_example.cwl                                   | 0
 tests/wc-tool-bad-hints.cwl                                 | 0
 tests/wc-tool-bad-reqs.cwl                                  | 0
 tests/wf/1496.cwl                                           | 1 +
 tests/wf/1590.cwl                                           | 1 +
 tests/wf/1st-workflow.cwl                                   | 0
 tests/wf/811-12.cwl                                         | 1 +
 tests/wf/811.cwl                                            | 1 +
 tests/wf/816_tool.cwl                                       | 1 +
 tests/wf/816_wf.cwl                                         | 1 +
 tests/wf/910.cwl                                            | 0
 tests/wf/arguments.cwl                                      | 0
 tests/wf/bad-stderr-expr.cwl                                | 0
 tests/wf/bad-stdin-expr.cwl                                 | 0
 tests/wf/bad-stdout-expr.cwl                                | 0
 tests/wf/bad_networkaccess.cwl                              | 0
 tests/wf/bad_timelimit.cwl                                  | 0
 tests/wf/cache_test_workflow.cwl                            | 0
 tests/wf/cat-tool.cwl                                       | 0
 tests/wf/conditional_step_no_inputs.cwl                     | 0
 tests/wf/conflict.cwl                                       | 0
 tests/wf/cores_float.cwl                                    | 0
 tests/wf/default-dir5.cwl                                   | 0
 tests/wf/default-wf5.cwl                                    | 0
 tests/wf/double-nested.cwl                                  | 0
 tests/wf/expect_trick_packed.cwl                            | 0
 tests/wf/extract_region_specs.cwl                           | 1 +
 tests/wf/floats_small_and_large.cwl                         | 1 +
 tests/wf/generator/pytoolgen.cwl                            | 0
 tests/wf/input_named_id.cwl                                 | 1 +
 tests/wf/iwd-passthrough1.cwl                               | 0
 tests/wf/iwdr-empty.cwl                                     | 0
 tests/wf/iwdr-entry.cwl                                     | 0
 tests/wf/iwdr-passthrough-successive.cwl                    | 0
 tests/wf/literalfile.cwl                                    | 0
 tests/wf/malformed_outputs.cwl                              | 0
 tests/wf/missing-tool.cwl                                   | 0
 tests/wf/mpi_env.cwl                                        | 0
 tests/wf/mpi_expr.cwl                                       | 0
 tests/wf/mpi_line_count.cwl                                 | 0
 tests/wf/mpi_simple.cwl                                     | 0
 tests/wf/mpi_simple_wf.cwl                                  | 0
 tests/wf/nested.cwl                                         | 0
 tests/wf/networkaccess-fail.cwl                             | 0
 tests/wf/networkaccess.cwl                                  | 0
 tests/wf/no-parameters-echo.cwl                             | 0
 tests/wf/nvidia-smi-cc.cwl                                  | 1 +
 tests/wf/nvidia-smi-container.cwl                           | 1 +
 tests/wf/nvidia-smi-max.cwl                                 | 1 +
 tests/wf/nvidia-smi-range.cwl                               | 1 +
 tests/wf/nvidia-smi.cwl                                     | 1 +
 tests/wf/operation/abstract-cosifer.cwl                     | 1 +
 tests/wf/operation/operation-single.cwl                     | 1 +
 tests/wf/optional-numerical-output-0.cwl                    | 0
 tests/wf/optional_src_mandatory_sink.cwl                    | 0
 tests/wf/packed-with-loadlisting.cwl                        | 0
 tests/wf/packed_no_main.cwl                                 | 1 +
 tests/wf/paramref_arguments_roundtrip.cwl                   | 0
 tests/wf/paramref_arguments_self.cwl                        | 0
 tests/wf/record_outputeval.cwl                              | 1 +
 tests/wf/resreq_expr_float_v1_0.cwl                         | 1 +
 tests/wf/resreq_expr_float_v1_2.cwl                         | 1 +
 tests/wf/scatter2.cwl                                       | 0
 tests/wf/scatter2_subwf.cwl                                 | 0
 tests/wf/schemadef-bug-1473.cwl                             | 1 +
 tests/wf/schemadef-tool-12.cwl                              | 0
 tests/wf/schemadef-tool.cwl                                 | 0
 tests/wf/sec-tool.cwl                                       | 0
 tests/wf/sec-wf-out.cwl                                     | 0
 tests/wf/sec-wf.cwl                                         | 0
 tests/wf/secret_job.cwl                                     | 0
 tests/wf/secret_wf.cwl                                      | 0
 tests/wf/separate_without_prefix.cwl                        | 0
 tests/wf/shm_size.cwl                                       | 0
 tests/wf/storage_float.cwl                                  | 0
 tests/wf/tar-param.cwl                                      | 0
 tests/wf/three_step_color.cwl                               | 0
 tests/wf/timelimit-fail.cwl                                 | 0
 tests/wf/timelimit.cwl                                      | 0
 tests/wf/touch_tool.cwl                                     | 0
 tests/wf/trick_defaults.cwl                                 | 0
 tests/wf/trick_defaults2.cwl                                | 0
 tests/wf/vf-concat.cwl                                      | 0
 tests/wf/workreuse-fail.cwl                                 | 0
 tests/wf/workreuse.cwl                                      | 0
 tests/with_doc.cwl                                          | 0
 tests/without_doc.cwl                                       | 0
 193 files changed, 37 insertions(+), 6 deletions(-)
 mode change 100644 => 100755 cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.1/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl
 mode change 100644 => 100755 cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl
 mode change 100644 => 100755 tests/CometAdapter.cwl
 mode change 100644 => 100755 tests/arg-empty-prefix-separate-false.cwl
 mode change 100644 => 100755 tests/checker_wf/optional_array_mismatch.cwl
 mode change 100644 => 100755 tests/default_values_list.cwl
 mode change 100644 => 100755 tests/echo-badposition-expr.cwl
 mode change 100644 => 100755 tests/echo-position-expr.cwl
 mode change 100644 => 100755 tests/echo-stdout-log-dir.cwl
 mode change 100644 => 100755 tests/env.cwl
 mode change 100644 => 100755 tests/env2.cwl
 mode change 100644 => 100755 tests/env3.cwl
 mode change 100644 => 100755 tests/env4.cwl
 mode change 100644 => 100755 tests/input_deps/docker-array-secondaryfiles.cwl
 mode change 100644 => 100755 tests/iwdr_bad_expr.cwl
 mode change 100644 => 100755 tests/iwdr_dir_literal_real_file.cwl
 mode change 100644 => 100755 tests/load_contents-array.cwl
 mode change 100644 => 100755 tests/loop-ext/all-output-loop-no-iteration.cwl
 mode change 100644 => 100755 tests/loop-ext/all-output-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/default-value-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-command-line-tool.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-expression-tool.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-hint.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-scatter.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-when-exception.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-when.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-loop-workflow.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-no-loopWhen.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-non-boolean-loopWhen.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-non-boolean-loopWhen2.cwl
 mode change 100644 => 100755 tests/loop-ext/invalid-value-from-loop-no-requirement.cwl
 mode change 100644 => 100755 tests/loop-ext/loop-inside-loop-all.cwl
 mode change 100644 => 100755 tests/loop-ext/loop-inside-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/loop-inside-scatter.cwl
 mode change 100644 => 100755 tests/loop-ext/multi-source-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/opt-var-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/scatter-inside-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/single-var-loop-no-iteration.cwl
 mode change 100644 => 100755 tests/loop-ext/single-var-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/two-vars-loop-2.cwl
 mode change 100644 => 100755 tests/loop-ext/two-vars-loop.cwl
 mode change 100644 => 100755 tests/loop-ext/value-from-loop.cwl
 mode change 100644 => 100755 tests/loop/all-output-loop-no-iteration.cwl
 mode change 100644 => 100755 tests/loop/all-output-loop.cwl
 mode change 100644 => 100755 tests/loop/default-value-loop.cwl
 mode change 100644 => 100755 tests/loop/invalid-loop-scatter.cwl
 mode change 100644 => 100755 tests/loop/invalid-loop-when-exception.cwl
 mode change 100644 => 100755 tests/loop/invalid-loop-when-exception2.cwl
 mode change 100644 => 100755 tests/loop/invalid-multi-source-loop-no-requirement.cwl
 mode change 100644 => 100755 tests/loop/invalid-no-loopWhen.cwl
 mode change 100644 => 100755 tests/loop/invalid-non-boolean-loopWhen.cwl
 mode change 100644 => 100755 tests/loop/invalid-non-boolean-loopWhen2.cwl
 mode change 100644 => 100755 tests/loop/invalid-value-from-loop-no-requirement.cwl
 mode change 100644 => 100755 tests/loop/loop-inside-loop-all.cwl
 mode change 100644 => 100755 tests/loop/loop-inside-loop.cwl
 mode change 100644 => 100755 tests/loop/loop-inside-scatter.cwl
 mode change 100644 => 100755 tests/loop/multi-source-loop.cwl
 mode change 100644 => 100755 tests/loop/opt-var-loop.cwl
 mode change 100644 => 100755 tests/loop/scatter-inside-loop.cwl
 mode change 100644 => 100755 tests/loop/single-var-loop-no-iteration.cwl
 mode change 100644 => 100755 tests/loop/single-var-loop.cwl
 mode change 100644 => 100755 tests/loop/two-vars-loop-2.cwl
 mode change 100644 => 100755 tests/loop/two-vars-loop.cwl
 mode change 100644 => 100755 tests/loop/value-from-loop.cwl
 mode change 100644 => 100755 tests/nested-array.cwl
 mode change 100644 => 100755 tests/non_portable.cwl
 mode change 100644 => 100755 tests/non_portable2.cwl
 mode change 100644 => 100755 tests/override/env-tool.cwl
 mode change 100644 => 100755 tests/override/env-tool_v1.1.0-dev1.cwl
 mode change 100644 => 100755 tests/override/env-tool_v1.1.cwl
 mode change 100644 => 100755 tests/portable.cwl
 mode change 100644 => 100755 tests/reloc/test.cwl
 mode change 100644 => 100755 tests/scatter_numbers.cwl
 mode change 100644 => 100755 tests/secondary-files-bad.cwl
 mode change 100644 => 100755 tests/secondary-files-required-container.cwl
 mode change 100644 => 100755 tests/secondary-files-required-missing-container.cwl
 mode change 100644 => 100755 tests/secondary-files-string-v1.cwl
 mode change 100644 => 100755 tests/secondary-files.cwl
 mode change 100644 => 100755 tests/sing_pullfolder_test.cwl
 mode change 100644 => 100755 tests/subgraph/1432.cwl
 mode change 100644 => 100755 tests/subgraph/env-tool2.cwl
 mode change 100644 => 100755 tests/subgraph/env-tool2_no_env.cwl
 mode change 100644 => 100755 tests/subgraph/env-tool2_req.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_hint_collision.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_hint_req_collision.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_long.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_only_hint.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_req_collision.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_subwf-packed.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_subwf.cwl
 mode change 100644 => 100755 tests/subgraph/env-wf2_subwf_b.cwl
 mode change 100644 => 100755 tests/subgraph/steplevel-resreq.cwl
 mode change 100644 => 100755 tests/subgraph/timelimit2-wf.cwl
 mode change 100644 => 100755 tests/trs/Dockstore.cwl
 mode change 100644 => 100755 tests/trs/md5sum-tool.cwl
 mode change 100644 => 100755 tests/trs/md5sum-workflow.cwl
 mode change 100644 => 100755 tests/utf_doc_example.cwl
 mode change 100644 => 100755 tests/wc-tool-bad-hints.cwl
 mode change 100644 => 100755 tests/wc-tool-bad-reqs.cwl
 mode change 100644 => 100755 tests/wf/1496.cwl
 mode change 100644 => 100755 tests/wf/1590.cwl
 mode change 100644 => 100755 tests/wf/1st-workflow.cwl
 mode change 100644 => 100755 tests/wf/811-12.cwl
 mode change 100644 => 100755 tests/wf/811.cwl
 mode change 100644 => 100755 tests/wf/816_tool.cwl
 mode change 100644 => 100755 tests/wf/816_wf.cwl
 mode change 100644 => 100755 tests/wf/910.cwl
 mode change 100644 => 100755 tests/wf/arguments.cwl
 mode change 100644 => 100755 tests/wf/bad-stderr-expr.cwl
 mode change 100644 => 100755 tests/wf/bad-stdin-expr.cwl
 mode change 100644 => 100755 tests/wf/bad-stdout-expr.cwl
 mode change 100644 => 100755 tests/wf/bad_networkaccess.cwl
 mode change 100644 => 100755 tests/wf/bad_timelimit.cwl
 mode change 100644 => 100755 tests/wf/cache_test_workflow.cwl
 mode change 100644 => 100755 tests/wf/cat-tool.cwl
 mode change 100644 => 100755 tests/wf/conditional_step_no_inputs.cwl
 mode change 100644 => 100755 tests/wf/conflict.cwl
 mode change 100644 => 100755 tests/wf/cores_float.cwl
 mode change 100644 => 100755 tests/wf/default-dir5.cwl
 mode change 100644 => 100755 tests/wf/default-wf5.cwl
 mode change 100644 => 100755 tests/wf/double-nested.cwl
 mode change 100644 => 100755 tests/wf/expect_trick_packed.cwl
 mode change 100644 => 100755 tests/wf/extract_region_specs.cwl
 mode change 100644 => 100755 tests/wf/floats_small_and_large.cwl
 mode change 100644 => 100755 tests/wf/generator/pytoolgen.cwl
 mode change 100644 => 100755 tests/wf/input_named_id.cwl
 mode change 100644 => 100755 tests/wf/iwd-passthrough1.cwl
 mode change 100644 => 100755 tests/wf/iwdr-empty.cwl
 mode change 100644 => 100755 tests/wf/iwdr-entry.cwl
 mode change 100644 => 100755 tests/wf/iwdr-passthrough-successive.cwl
 mode change 100644 => 100755 tests/wf/literalfile.cwl
 mode change 100644 => 100755 tests/wf/malformed_outputs.cwl
 mode change 100644 => 100755 tests/wf/missing-tool.cwl
 mode change 100644 => 100755 tests/wf/mpi_env.cwl
 mode change 100644 => 100755 tests/wf/mpi_expr.cwl
 mode change 100644 => 100755 tests/wf/mpi_line_count.cwl
 mode change 100644 => 100755 tests/wf/mpi_simple.cwl
 mode change 100644 => 100755 tests/wf/mpi_simple_wf.cwl
 mode change 100644 => 100755 tests/wf/nested.cwl
 mode change 100644 => 100755 tests/wf/networkaccess-fail.cwl
 mode change 100644 => 100755 tests/wf/networkaccess.cwl
 mode change 100644 => 100755 tests/wf/no-parameters-echo.cwl
 mode change 100644 => 100755 tests/wf/nvidia-smi-cc.cwl
 mode change 100644 => 100755 tests/wf/nvidia-smi-container.cwl
 mode change 100644 => 100755 tests/wf/nvidia-smi-max.cwl
 mode change 100644 => 100755 tests/wf/nvidia-smi-range.cwl
 mode change 100644 => 100755 tests/wf/nvidia-smi.cwl
 mode change 100644 => 100755 tests/wf/operation/abstract-cosifer.cwl
 mode change 100644 => 100755 tests/wf/operation/operation-single.cwl
 mode change 100644 => 100755 tests/wf/optional-numerical-output-0.cwl
 mode change 100644 => 100755 tests/wf/optional_src_mandatory_sink.cwl
 mode change 100644 => 100755 tests/wf/packed-with-loadlisting.cwl
 mode change 100644 => 100755 tests/wf/packed_no_main.cwl
 mode change 100644 => 100755 tests/wf/paramref_arguments_roundtrip.cwl
 mode change 100644 => 100755 tests/wf/paramref_arguments_self.cwl
 mode change 100644 => 100755 tests/wf/record_outputeval.cwl
 mode change 100644 => 100755 tests/wf/resreq_expr_float_v1_0.cwl
 mode change 100644 => 100755 tests/wf/resreq_expr_float_v1_2.cwl
 mode change 100644 => 100755 tests/wf/scatter2.cwl
 mode change 100644 => 100755 tests/wf/scatter2_subwf.cwl
 mode change 100644 => 100755 tests/wf/schemadef-bug-1473.cwl
 mode change 100644 => 100755 tests/wf/schemadef-tool-12.cwl
 mode change 100644 => 100755 tests/wf/schemadef-tool.cwl
 mode change 100644 => 100755 tests/wf/sec-tool.cwl
 mode change 100644 => 100755 tests/wf/sec-wf-out.cwl
 mode change 100644 => 100755 tests/wf/sec-wf.cwl
 mode change 100644 => 100755 tests/wf/secret_job.cwl
 mode change 100644 => 100755 tests/wf/secret_wf.cwl
 mode change 100644 => 100755 tests/wf/separate_without_prefix.cwl
 mode change 100644 => 100755 tests/wf/shm_size.cwl
 mode change 100644 => 100755 tests/wf/storage_float.cwl
 mode change 100644 => 100755 tests/wf/tar-param.cwl
 mode change 100644 => 100755 tests/wf/three_step_color.cwl
 mode change 100644 => 100755 tests/wf/timelimit-fail.cwl
 mode change 100644 => 100755 tests/wf/timelimit.cwl
 mode change 100644 => 100755 tests/wf/touch_tool.cwl
 mode change 100644 => 100755 tests/wf/trick_defaults.cwl
 mode change 100644 => 100755 tests/wf/trick_defaults2.cwl
 mode change 100644 => 100755 tests/wf/vf-concat.cwl
 mode change 100644 => 100755 tests/wf/workreuse-fail.cwl
 mode change 100644 => 100755 tests/wf/workreuse.cwl
 mode change 100644 => 100755 tests/with_doc.cwl
 mode change 100644 => 100755 tests/without_doc.cwl

diff --git a/cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.1/cwl-runner.cwl b/cwltool/schemas/v1.1/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl b/cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl b/cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl
old mode 100644
new mode 100755
diff --git a/tests/CometAdapter.cwl b/tests/CometAdapter.cwl
old mode 100644
new mode 100755
index ed1b24b..3d70835
--- a/tests/CometAdapter.cwl
+++ b/tests/CometAdapter.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 # Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
 # SPDX-License-Identifier: Apache-2.0
 label: CometAdapter
diff --git a/tests/arg-empty-prefix-separate-false.cwl b/tests/arg-empty-prefix-separate-false.cwl
old mode 100644
new mode 100755
diff --git a/tests/checker_wf/optional_array_mismatch.cwl b/tests/checker_wf/optional_array_mismatch.cwl
old mode 100644
new mode 100755
index d6f0527..a557927
--- a/tests/checker_wf/optional_array_mismatch.cwl
+++ b/tests/checker_wf/optional_array_mismatch.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs:
diff --git a/tests/default_values_list.cwl b/tests/default_values_list.cwl
old mode 100644
new mode 100755
diff --git a/tests/echo-badposition-expr.cwl b/tests/echo-badposition-expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/echo-position-expr.cwl b/tests/echo-position-expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/echo-stdout-log-dir.cwl b/tests/echo-stdout-log-dir.cwl
old mode 100644
new mode 100755
diff --git a/tests/env.cwl b/tests/env.cwl
old mode 100644
new mode 100755
diff --git a/tests/env2.cwl b/tests/env2.cwl
old mode 100644
new mode 100755
diff --git a/tests/env3.cwl b/tests/env3.cwl
old mode 100644
new mode 100755
diff --git a/tests/env4.cwl b/tests/env4.cwl
old mode 100644
new mode 100755
diff --git a/tests/input_deps/docker-array-secondaryfiles.cwl b/tests/input_deps/docker-array-secondaryfiles.cwl
old mode 100644
new mode 100755
diff --git a/tests/iwdr_bad_expr.cwl b/tests/iwdr_bad_expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/iwdr_dir_literal_real_file.cwl b/tests/iwdr_dir_literal_real_file.cwl
old mode 100644
new mode 100755
diff --git a/tests/load_contents-array.cwl b/tests/load_contents-array.cwl
old mode 100644
new mode 100755
index f6b786e..eaad624
--- a/tests/load_contents-array.cwl
+++ b/tests/load_contents-array.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: "v1.2"
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/loop-ext/all-output-loop-no-iteration.cwl b/tests/loop-ext/all-output-loop-no-iteration.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/all-output-loop.cwl b/tests/loop-ext/all-output-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/default-value-loop.cwl b/tests/loop-ext/default-value-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-command-line-tool.cwl b/tests/loop-ext/invalid-loop-command-line-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-expression-tool.cwl b/tests/loop-ext/invalid-loop-expression-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-hint.cwl b/tests/loop-ext/invalid-loop-hint.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-scatter.cwl b/tests/loop-ext/invalid-loop-scatter.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-when-exception.cwl b/tests/loop-ext/invalid-loop-when-exception.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-when.cwl b/tests/loop-ext/invalid-loop-when.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-loop-workflow.cwl b/tests/loop-ext/invalid-loop-workflow.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl b/tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-no-loopWhen.cwl b/tests/loop-ext/invalid-no-loopWhen.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-non-boolean-loopWhen.cwl b/tests/loop-ext/invalid-non-boolean-loopWhen.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-non-boolean-loopWhen2.cwl b/tests/loop-ext/invalid-non-boolean-loopWhen2.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/invalid-value-from-loop-no-requirement.cwl b/tests/loop-ext/invalid-value-from-loop-no-requirement.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/loop-inside-loop-all.cwl b/tests/loop-ext/loop-inside-loop-all.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/loop-inside-loop.cwl b/tests/loop-ext/loop-inside-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/loop-inside-scatter.cwl b/tests/loop-ext/loop-inside-scatter.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/multi-source-loop.cwl b/tests/loop-ext/multi-source-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/opt-var-loop.cwl b/tests/loop-ext/opt-var-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/scatter-inside-loop.cwl b/tests/loop-ext/scatter-inside-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/single-var-loop-no-iteration.cwl b/tests/loop-ext/single-var-loop-no-iteration.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/single-var-loop.cwl b/tests/loop-ext/single-var-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/two-vars-loop-2.cwl b/tests/loop-ext/two-vars-loop-2.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/two-vars-loop.cwl b/tests/loop-ext/two-vars-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop-ext/value-from-loop.cwl b/tests/loop-ext/value-from-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/all-output-loop-no-iteration.cwl b/tests/loop/all-output-loop-no-iteration.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/all-output-loop.cwl b/tests/loop/all-output-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/default-value-loop.cwl b/tests/loop/default-value-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-loop-scatter.cwl b/tests/loop/invalid-loop-scatter.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-loop-when-exception.cwl b/tests/loop/invalid-loop-when-exception.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-loop-when-exception2.cwl b/tests/loop/invalid-loop-when-exception2.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-multi-source-loop-no-requirement.cwl b/tests/loop/invalid-multi-source-loop-no-requirement.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-no-loopWhen.cwl b/tests/loop/invalid-no-loopWhen.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-non-boolean-loopWhen.cwl b/tests/loop/invalid-non-boolean-loopWhen.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-non-boolean-loopWhen2.cwl b/tests/loop/invalid-non-boolean-loopWhen2.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/invalid-value-from-loop-no-requirement.cwl b/tests/loop/invalid-value-from-loop-no-requirement.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/loop-inside-loop-all.cwl b/tests/loop/loop-inside-loop-all.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/loop-inside-loop.cwl b/tests/loop/loop-inside-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/loop-inside-scatter.cwl b/tests/loop/loop-inside-scatter.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/multi-source-loop.cwl b/tests/loop/multi-source-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/opt-var-loop.cwl b/tests/loop/opt-var-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/scatter-inside-loop.cwl b/tests/loop/scatter-inside-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/single-var-loop-no-iteration.cwl b/tests/loop/single-var-loop-no-iteration.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/single-var-loop.cwl b/tests/loop/single-var-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/two-vars-loop-2.cwl b/tests/loop/two-vars-loop-2.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/two-vars-loop.cwl b/tests/loop/two-vars-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/loop/value-from-loop.cwl b/tests/loop/value-from-loop.cwl
old mode 100644
new mode 100755
diff --git a/tests/nested-array.cwl b/tests/nested-array.cwl
old mode 100644
new mode 100755
index 8272614..6aa3650
--- a/tests/nested-array.cwl
+++ b/tests/nested-array.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/non_portable.cwl b/tests/non_portable.cwl
old mode 100644
new mode 100755
diff --git a/tests/non_portable2.cwl b/tests/non_portable2.cwl
old mode 100644
new mode 100755
diff --git a/tests/override/env-tool.cwl b/tests/override/env-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/override/env-tool_v1.1.0-dev1.cwl b/tests/override/env-tool_v1.1.0-dev1.cwl
old mode 100644
new mode 100755
diff --git a/tests/override/env-tool_v1.1.cwl b/tests/override/env-tool_v1.1.cwl
old mode 100644
new mode 100755
diff --git a/tests/portable.cwl b/tests/portable.cwl
old mode 100644
new mode 100755
diff --git a/tests/reloc/test.cwl b/tests/reloc/test.cwl
old mode 100644
new mode 100755
index 41d3747..c88cf48
--- a/tests/reloc/test.cwl
+++ b/tests/reloc/test.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 inputs:
diff --git a/tests/scatter_numbers.cwl b/tests/scatter_numbers.cwl
old mode 100644
new mode 100755
diff --git a/tests/secondary-files-bad.cwl b/tests/secondary-files-bad.cwl
old mode 100644
new mode 100755
diff --git a/tests/secondary-files-required-container.cwl b/tests/secondary-files-required-container.cwl
old mode 100644
new mode 100755
diff --git a/tests/secondary-files-required-missing-container.cwl b/tests/secondary-files-required-missing-container.cwl
old mode 100644
new mode 100755
diff --git a/tests/secondary-files-string-v1.cwl b/tests/secondary-files-string-v1.cwl
old mode 100644
new mode 100755
diff --git a/tests/secondary-files.cwl b/tests/secondary-files.cwl
old mode 100644
new mode 100755
diff --git a/tests/sing_pullfolder_test.cwl b/tests/sing_pullfolder_test.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/1432.cwl b/tests/subgraph/1432.cwl
old mode 100644
new mode 100755
index 54d5538..41283ab
--- a/tests/subgraph/1432.cwl
+++ b/tests/subgraph/1432.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.2
 inputs:
diff --git a/tests/subgraph/env-tool2.cwl b/tests/subgraph/env-tool2.cwl
old mode 100644
new mode 100755
index f568e54..14c8a68
--- a/tests/subgraph/env-tool2.cwl
+++ b/tests/subgraph/env-tool2.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.2
 inputs:
diff --git a/tests/subgraph/env-tool2_no_env.cwl b/tests/subgraph/env-tool2_no_env.cwl
old mode 100644
new mode 100755
index c4a6f63..2b3711b
--- a/tests/subgraph/env-tool2_no_env.cwl
+++ b/tests/subgraph/env-tool2_no_env.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.2
 inputs:
diff --git a/tests/subgraph/env-tool2_req.cwl b/tests/subgraph/env-tool2_req.cwl
old mode 100644
new mode 100755
index 96b0bc3..9431080
--- a/tests/subgraph/env-tool2_req.cwl
+++ b/tests/subgraph/env-tool2_req.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.2
 inputs:
diff --git a/tests/subgraph/env-wf2.cwl b/tests/subgraph/env-wf2.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_hint_collision.cwl b/tests/subgraph/env-wf2_hint_collision.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_hint_req_collision.cwl b/tests/subgraph/env-wf2_hint_req_collision.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_long.cwl b/tests/subgraph/env-wf2_long.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_only_hint.cwl b/tests/subgraph/env-wf2_only_hint.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_req_collision.cwl b/tests/subgraph/env-wf2_req_collision.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_subwf-packed.cwl b/tests/subgraph/env-wf2_subwf-packed.cwl
old mode 100644
new mode 100755
index ed119f0..e1c0964
--- a/tests/subgraph/env-wf2_subwf-packed.cwl
+++ b/tests/subgraph/env-wf2_subwf-packed.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
     "$graph": [
         {
@@ -127,4 +128,4 @@
         }
     ],
     "cwlVersion": "v1.2"
-}
\ No newline at end of file
+}
diff --git a/tests/subgraph/env-wf2_subwf.cwl b/tests/subgraph/env-wf2_subwf.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/env-wf2_subwf_b.cwl b/tests/subgraph/env-wf2_subwf_b.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/steplevel-resreq.cwl b/tests/subgraph/steplevel-resreq.cwl
old mode 100644
new mode 100755
diff --git a/tests/subgraph/timelimit2-wf.cwl b/tests/subgraph/timelimit2-wf.cwl
old mode 100644
new mode 100755
diff --git a/tests/test_examples.py b/tests/test_examples.py
index f413976..b78965b 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -1878,7 +1878,7 @@ def test_invalid_nested_array() -> None:
     stdout = re.sub(r"\s\s+", " ", stdout)
     assert "Tool definition failed validation:" in stdout
     assert (
-        "tests/nested-array.cwl:6:5: Field 'type' references unknown identifier 'string[][]'"
+        "tests/nested-array.cwl:7:5: Field 'type' references unknown identifier 'string[][]'"
     ) in stdout
 
 
diff --git a/tests/test_validate.py b/tests/test_validate.py
index f2d89e4..8e664d9 100644
--- a/tests/test_validate.py
+++ b/tests/test_validate.py
@@ -70,7 +70,7 @@ def test_validate_quiet() -> None:
     stdout = re.sub(r"\s\s+", " ", stdout)
     assert "INFO" not in stdout
     assert "INFO" not in stderr
-    assert "tests/CometAdapter.cwl:9:3: object id" in stdout
+    assert "tests/CometAdapter.cwl:10:3: object id" in stdout
     assert "tests/CometAdapter.cwl#out' previously defined" in stdout
 
 
@@ -119,9 +119,9 @@ def test_validate_custom_logger() -> None:
     assert "WARNING" not in stdout
     assert "WARNING" not in stderr
     assert "WARNING" in custom_log_text
-    assert "tests/CometAdapter.cwl:9:3: object id" not in stdout
-    assert "tests/CometAdapter.cwl:9:3: object id" not in stderr
-    assert "tests/CometAdapter.cwl:9:3: object id" in custom_log_text
+    assert "tests/CometAdapter.cwl:10:3: object id" not in stdout
+    assert "tests/CometAdapter.cwl:10:3: object id" not in stderr
+    assert "tests/CometAdapter.cwl:10:3: object id" in custom_log_text
     assert "tests/CometAdapter.cwl#out' previously defined" not in stdout
     assert "tests/CometAdapter.cwl#out' previously defined" not in stderr
     assert "tests/CometAdapter.cwl#out' previously defined" in custom_log_text
diff --git a/tests/trs/Dockstore.cwl b/tests/trs/Dockstore.cwl
old mode 100644
new mode 100755
diff --git a/tests/trs/md5sum-tool.cwl b/tests/trs/md5sum-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/trs/md5sum-workflow.cwl b/tests/trs/md5sum-workflow.cwl
old mode 100644
new mode 100755
diff --git a/tests/utf_doc_example.cwl b/tests/utf_doc_example.cwl
old mode 100644
new mode 100755
diff --git a/tests/wc-tool-bad-hints.cwl b/tests/wc-tool-bad-hints.cwl
old mode 100644
new mode 100755
diff --git a/tests/wc-tool-bad-reqs.cwl b/tests/wc-tool-bad-reqs.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/1496.cwl b/tests/wf/1496.cwl
old mode 100644
new mode 100755
index 74f6ef4..d5da025
--- a/tests/wf/1496.cwl
+++ b/tests/wf/1496.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 
diff --git a/tests/wf/1590.cwl b/tests/wf/1590.cwl
old mode 100644
new mode 100755
index 19c8ad3..de602a5
--- a/tests/wf/1590.cwl
+++ b/tests/wf/1590.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
   "baseCommand": [
     "cat"
diff --git a/tests/wf/1st-workflow.cwl b/tests/wf/1st-workflow.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/811-12.cwl b/tests/wf/811-12.cwl
old mode 100644
new mode 100755
index f4403f4..ab0b2bd
--- a/tests/wf/811-12.cwl
+++ b/tests/wf/811-12.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: Workflow
 
diff --git a/tests/wf/811.cwl b/tests/wf/811.cwl
old mode 100644
new mode 100755
index 16a4c82..8ef826f
--- a/tests/wf/811.cwl
+++ b/tests/wf/811.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 
diff --git a/tests/wf/816_tool.cwl b/tests/wf/816_tool.cwl
old mode 100644
new mode 100755
index 00395ab..c48d3e3
--- a/tests/wf/816_tool.cwl
+++ b/tests/wf/816_tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
diff --git a/tests/wf/816_wf.cwl b/tests/wf/816_wf.cwl
old mode 100644
new mode 100755
index a64b130..9db1439
--- a/tests/wf/816_wf.cwl
+++ b/tests/wf/816_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs:
diff --git a/tests/wf/910.cwl b/tests/wf/910.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/arguments.cwl b/tests/wf/arguments.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/bad-stderr-expr.cwl b/tests/wf/bad-stderr-expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/bad-stdin-expr.cwl b/tests/wf/bad-stdin-expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/bad-stdout-expr.cwl b/tests/wf/bad-stdout-expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/bad_networkaccess.cwl b/tests/wf/bad_networkaccess.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/bad_timelimit.cwl b/tests/wf/bad_timelimit.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/cache_test_workflow.cwl b/tests/wf/cache_test_workflow.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/cat-tool.cwl b/tests/wf/cat-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/conditional_step_no_inputs.cwl b/tests/wf/conditional_step_no_inputs.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/conflict.cwl b/tests/wf/conflict.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/cores_float.cwl b/tests/wf/cores_float.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/default-dir5.cwl b/tests/wf/default-dir5.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/default-wf5.cwl b/tests/wf/default-wf5.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/double-nested.cwl b/tests/wf/double-nested.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/expect_trick_packed.cwl b/tests/wf/expect_trick_packed.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/extract_region_specs.cwl b/tests/wf/extract_region_specs.cwl
old mode 100644
new mode 100755
index 279fa44..437222a
--- a/tests/wf/extract_region_specs.cwl
+++ b/tests/wf/extract_region_specs.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
 "cwlVersion": "v1.0",
 "class": "CommandLineTool",
diff --git a/tests/wf/floats_small_and_large.cwl b/tests/wf/floats_small_and_large.cwl
old mode 100644
new mode 100755
index 4343273..1637bd9
--- a/tests/wf/floats_small_and_large.cwl
+++ b/tests/wf/floats_small_and_large.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/wf/generator/pytoolgen.cwl b/tests/wf/generator/pytoolgen.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/input_named_id.cwl b/tests/wf/input_named_id.cwl
old mode 100644
new mode 100755
index e559f96..82a0353
--- a/tests/wf/input_named_id.cwl
+++ b/tests/wf/input_named_id.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 label: FeatureFinderIdentification
 doc: ""
 inputs:
diff --git a/tests/wf/iwd-passthrough1.cwl b/tests/wf/iwd-passthrough1.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/iwdr-empty.cwl b/tests/wf/iwdr-empty.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/iwdr-entry.cwl b/tests/wf/iwdr-entry.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/iwdr-passthrough-successive.cwl b/tests/wf/iwdr-passthrough-successive.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/literalfile.cwl b/tests/wf/literalfile.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/malformed_outputs.cwl b/tests/wf/malformed_outputs.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/missing-tool.cwl b/tests/wf/missing-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/mpi_env.cwl b/tests/wf/mpi_env.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/mpi_expr.cwl b/tests/wf/mpi_expr.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/mpi_line_count.cwl b/tests/wf/mpi_line_count.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/mpi_simple.cwl b/tests/wf/mpi_simple.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/mpi_simple_wf.cwl b/tests/wf/mpi_simple_wf.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/nested.cwl b/tests/wf/nested.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/networkaccess-fail.cwl b/tests/wf/networkaccess-fail.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/networkaccess.cwl b/tests/wf/networkaccess.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/no-parameters-echo.cwl b/tests/wf/no-parameters-echo.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/nvidia-smi-cc.cwl b/tests/wf/nvidia-smi-cc.cwl
old mode 100644
new mode 100755
index a4f315b..92e781d
--- a/tests/wf/nvidia-smi-cc.cwl
+++ b/tests/wf/nvidia-smi-cc.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/nvidia-smi-container.cwl b/tests/wf/nvidia-smi-container.cwl
old mode 100644
new mode 100755
index 84fd72d..22092fa
--- a/tests/wf/nvidia-smi-container.cwl
+++ b/tests/wf/nvidia-smi-container.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/nvidia-smi-max.cwl b/tests/wf/nvidia-smi-max.cwl
old mode 100644
new mode 100755
index d3d4d5e..1f8687d
--- a/tests/wf/nvidia-smi-max.cwl
+++ b/tests/wf/nvidia-smi-max.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/nvidia-smi-range.cwl b/tests/wf/nvidia-smi-range.cwl
old mode 100644
new mode 100755
index 19d3ea4..2e131a3
--- a/tests/wf/nvidia-smi-range.cwl
+++ b/tests/wf/nvidia-smi-range.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/nvidia-smi.cwl b/tests/wf/nvidia-smi.cwl
old mode 100644
new mode 100755
index 8e227d0..8a17f8e
--- a/tests/wf/nvidia-smi.cwl
+++ b/tests/wf/nvidia-smi.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/operation/abstract-cosifer.cwl b/tests/wf/operation/abstract-cosifer.cwl
old mode 100644
new mode 100755
index 0576208..2a50cde
--- a/tests/wf/operation/abstract-cosifer.cwl
+++ b/tests/wf/operation/abstract-cosifer.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Operation
 cwlVersion: v1.2
 
diff --git a/tests/wf/operation/operation-single.cwl b/tests/wf/operation/operation-single.cwl
old mode 100644
new mode 100755
index 2119bf0..63b6a6b
--- a/tests/wf/operation/operation-single.cwl
+++ b/tests/wf/operation/operation-single.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.2
 id: abstract_cosifer_workflow
diff --git a/tests/wf/optional-numerical-output-0.cwl b/tests/wf/optional-numerical-output-0.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/optional_src_mandatory_sink.cwl b/tests/wf/optional_src_mandatory_sink.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/packed-with-loadlisting.cwl b/tests/wf/packed-with-loadlisting.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/packed_no_main.cwl b/tests/wf/packed_no_main.cwl
old mode 100644
new mode 100755
index 8307a08..aafd0de
--- a/tests/wf/packed_no_main.cwl
+++ b/tests/wf/packed_no_main.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 $graph:
 - id: echo
diff --git a/tests/wf/paramref_arguments_roundtrip.cwl b/tests/wf/paramref_arguments_roundtrip.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/paramref_arguments_self.cwl b/tests/wf/paramref_arguments_self.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/record_outputeval.cwl b/tests/wf/record_outputeval.cwl
old mode 100644
new mode 100755
index 45daf9b..e7b59cb
--- a/tests/wf/record_outputeval.cwl
+++ b/tests/wf/record_outputeval.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 requirements:
diff --git a/tests/wf/resreq_expr_float_v1_0.cwl b/tests/wf/resreq_expr_float_v1_0.cwl
old mode 100644
new mode 100755
index d5ea08c..a36877c
--- a/tests/wf/resreq_expr_float_v1_0.cwl
+++ b/tests/wf/resreq_expr_float_v1_0.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
diff --git a/tests/wf/resreq_expr_float_v1_2.cwl b/tests/wf/resreq_expr_float_v1_2.cwl
old mode 100644
new mode 100755
index cfb1b2a..ca72364
--- a/tests/wf/resreq_expr_float_v1_2.cwl
+++ b/tests/wf/resreq_expr_float_v1_2.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.2
 class: CommandLineTool
 requirements:
diff --git a/tests/wf/scatter2.cwl b/tests/wf/scatter2.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/scatter2_subwf.cwl b/tests/wf/scatter2_subwf.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/schemadef-bug-1473.cwl b/tests/wf/schemadef-bug-1473.cwl
old mode 100644
new mode 100755
index ad87ae0..beab321
--- a/tests/wf/schemadef-bug-1473.cwl
+++ b/tests/wf/schemadef-bug-1473.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
     "$graph": [
         {
diff --git a/tests/wf/schemadef-tool-12.cwl b/tests/wf/schemadef-tool-12.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/schemadef-tool.cwl b/tests/wf/schemadef-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/sec-tool.cwl b/tests/wf/sec-tool.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/sec-wf-out.cwl b/tests/wf/sec-wf-out.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/sec-wf.cwl b/tests/wf/sec-wf.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/secret_job.cwl b/tests/wf/secret_job.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/secret_wf.cwl b/tests/wf/secret_wf.cwl
old mode 100644
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diff --git a/tests/wf/separate_without_prefix.cwl b/tests/wf/separate_without_prefix.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/shm_size.cwl b/tests/wf/shm_size.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/storage_float.cwl b/tests/wf/storage_float.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/tar-param.cwl b/tests/wf/tar-param.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/three_step_color.cwl b/tests/wf/three_step_color.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/timelimit-fail.cwl b/tests/wf/timelimit-fail.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/timelimit.cwl b/tests/wf/timelimit.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/touch_tool.cwl b/tests/wf/touch_tool.cwl
old mode 100644
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diff --git a/tests/wf/trick_defaults.cwl b/tests/wf/trick_defaults.cwl
old mode 100644
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diff --git a/tests/wf/trick_defaults2.cwl b/tests/wf/trick_defaults2.cwl
old mode 100644
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diff --git a/tests/wf/vf-concat.cwl b/tests/wf/vf-concat.cwl
old mode 100644
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diff --git a/tests/wf/workreuse-fail.cwl b/tests/wf/workreuse-fail.cwl
old mode 100644
new mode 100755
diff --git a/tests/wf/workreuse.cwl b/tests/wf/workreuse.cwl
old mode 100644
new mode 100755
diff --git a/tests/with_doc.cwl b/tests/with_doc.cwl
old mode 100644
new mode 100755
diff --git a/tests/without_doc.cwl b/tests/without_doc.cwl
old mode 100644
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