From 726c1b4ff9885b22615baa6f59f7ff72b8587b35 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 30 Jan 2025 11:15:09 +0100 Subject: [PATCH] Add missing cwl-runner refs 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 .../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 ed1b24bb6..3d7083560 --- 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 d6f052757..a557927f2 --- 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 f6b786ec6..eaad62436 --- 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 8272614fc..6aa3650b8 --- 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 41d37474e..c88cf48da --- 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 54d553875..41283abfe --- 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 f568e5450..14c8a6826 --- 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 c4a6f6327..2b3711b77 --- 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 96b0bc3d1..943108056 --- 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 ed119f0f2..e1c09649d --- 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 f413976fd..b78965bb4 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 f2d89e473..8e664d9aa 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 74f6ef49e..d5da025dd --- 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 19c8ad331..de602a500 --- 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 f4403f45b..ab0b2bd92 --- 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 16a4c828d..8ef826fdc --- 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 00395abe8..c48d3e373 --- 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 a64b130b6..9db143916 --- 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 279fa4400..437222a13 --- 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 434327361..1637bd9af --- 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 e559f967b..82a0353aa --- 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 a4f315b0e..92e781d26 --- 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 84fd72d83..22092fae4 --- 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 d3d4d5e9c..1f8687d4d --- 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 19d3ea43c..2e131a373 --- 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 8e227d0c5..8a17f8e17 --- 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 057620844..2a50cded7 --- 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 2119bf02e..63b6a6bf0 --- 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 8307a083e..aafd0de58 --- 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 $graph: - id: echo diff --git a/tests/wf/paramref_arguments_roundtrip.cwl b/tests/wf/paramref_arguments_roundtrip.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/paramref_arguments_self.cwl b/tests/wf/paramref_arguments_self.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/record_outputeval.cwl b/tests/wf/record_outputeval.cwl old mode 100644 new mode 100755 index 45daf9b4d..e7b59cb6c --- a/tests/wf/record_outputeval.cwl +++ b/tests/wf/record_outputeval.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.2 class: CommandLineTool requirements: diff --git a/tests/wf/resreq_expr_float_v1_0.cwl b/tests/wf/resreq_expr_float_v1_0.cwl old mode 100644 new mode 100755 index d5ea08cde..a36877c0f --- a/tests/wf/resreq_expr_float_v1_0.cwl +++ b/tests/wf/resreq_expr_float_v1_0.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: CommandLineTool requirements: diff --git a/tests/wf/resreq_expr_float_v1_2.cwl b/tests/wf/resreq_expr_float_v1_2.cwl old mode 100644 new mode 100755 index cfb1b2a13..ca72364b7 --- a/tests/wf/resreq_expr_float_v1_2.cwl +++ b/tests/wf/resreq_expr_float_v1_2.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.2 class: CommandLineTool requirements: diff --git a/tests/wf/scatter2.cwl b/tests/wf/scatter2.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/scatter2_subwf.cwl b/tests/wf/scatter2_subwf.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/schemadef-bug-1473.cwl b/tests/wf/schemadef-bug-1473.cwl old mode 100644 new mode 100755 index ad87ae08e..beab3211d --- a/tests/wf/schemadef-bug-1473.cwl +++ b/tests/wf/schemadef-bug-1473.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner { "$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 new mode 100755 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 new mode 100755 diff --git a/tests/wf/trick_defaults.cwl b/tests/wf/trick_defaults.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/trick_defaults2.cwl b/tests/wf/trick_defaults2.cwl old mode 100644 new mode 100755 diff --git a/tests/wf/vf-concat.cwl b/tests/wf/vf-concat.cwl old mode 100644 new mode 100755 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 new mode 100755