diff --git a/testdata/cond-single-source-wf-003.1.cwl b/testdata/cond-single-source-wf-003.1.cwl old mode 100644 new mode 100755 index e6f24542..78e780d9 --- a/testdata/cond-single-source-wf-003.1.cwl +++ b/testdata/cond-single-source-wf-003.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: diff --git a/testdata/cond-single-source-wf-004.1.cwl b/testdata/cond-single-source-wf-004.1.cwl old mode 100644 new mode 100755 index c535eb94..0d48f276 --- a/testdata/cond-single-source-wf-004.1.cwl +++ b/testdata/cond-single-source-wf-004.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: @@ -20,4 +21,4 @@ outputs: pickValue: the_only_non_null requirements: - InlineJavascriptRequirement: {} \ No newline at end of file + InlineJavascriptRequirement: {} diff --git a/testdata/cond-single-source-wf-005.1.cwl b/testdata/cond-single-source-wf-005.1.cwl old mode 100644 new mode 100755 index 9503e31c..ab9bd75c --- a/testdata/cond-single-source-wf-005.1.cwl +++ b/testdata/cond-single-source-wf-005.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: @@ -20,4 +21,4 @@ outputs: pickValue: all_non_null requirements: - InlineJavascriptRequirement: {} \ No newline at end of file + InlineJavascriptRequirement: {} diff --git a/testdata/cond-wf-003.1.cwl b/testdata/cond-wf-003.1.cwl old mode 100644 new mode 100755 index cd04dbb5..1a223fbe --- a/testdata/cond-wf-003.1.cwl +++ b/testdata/cond-wf-003.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: diff --git a/testdata/cond-wf-004.1.cwl b/testdata/cond-wf-004.1.cwl old mode 100644 new mode 100755 index 4aea6fb4..2ad67d54 --- a/testdata/cond-wf-004.1.cwl +++ b/testdata/cond-wf-004.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: @@ -31,4 +32,4 @@ outputs: requirements: InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} \ No newline at end of file + MultipleInputFeatureRequirement: {} diff --git a/testdata/cond-wf-005.1.cwl b/testdata/cond-wf-005.1.cwl old mode 100644 new mode 100755 index 9b7af721..005c74c9 --- a/testdata/cond-wf-005.1.cwl +++ b/testdata/cond-wf-005.1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 inputs: @@ -31,4 +32,4 @@ outputs: requirements: InlineJavascriptRequirement: {} - MultipleInputFeatureRequirement: {} \ No newline at end of file + MultipleInputFeatureRequirement: {} diff --git a/testdata/count-lines6-single-source-wf_v1_0.cwl b/testdata/count-lines6-single-source-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines6-single-source-wf_v1_1.cwl b/testdata/count-lines6-single-source-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines6-single-source-wf_v1_2.cwl b/testdata/count-lines6-single-source-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines6-wf_v1_0.cwl b/testdata/count-lines6-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines6-wf_v1_1.cwl b/testdata/count-lines6-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines6-wf_v1_2.cwl b/testdata/count-lines6-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-single-source-wf_v1_0.cwl b/testdata/count-lines7-single-source-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-single-source-wf_v1_1.cwl b/testdata/count-lines7-single-source-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-single-source-wf_v1_2.cwl b/testdata/count-lines7-single-source-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-wf_v1_0.cwl b/testdata/count-lines7-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-wf_v1_1.cwl b/testdata/count-lines7-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/count-lines7-wf_v1_2.cwl b/testdata/count-lines7-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/dockstore-tool-md5sum.cwl b/testdata/dockstore-tool-md5sum.cwl old mode 100644 new mode 100755 diff --git a/testdata/dockstore-tool-md5sum_v11.cwl b/testdata/dockstore-tool-md5sum_v11.cwl old mode 100644 new mode 100755 diff --git a/testdata/dockstore-tool-md5sum_v12.cwl b/testdata/dockstore-tool-md5sum_v12.cwl old mode 100644 new mode 100755 diff --git a/testdata/echo-tool-packed.cwl b/testdata/echo-tool-packed.cwl old mode 100644 new mode 100755 index f9f2c336..108f57a2 --- a/testdata/echo-tool-packed.cwl +++ b/testdata/echo-tool-packed.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.2 $graph: - class: CommandLineTool diff --git a/testdata/foo-array.cwl b/testdata/foo-array.cwl old mode 100644 new mode 100755 index 4c8997b5..81c675ea --- a/testdata/foo-array.cwl +++ b/testdata/foo-array.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: v1.2 inputs: diff --git a/testdata/foo.cwl b/testdata/foo.cwl old mode 100644 new mode 100755 index 9e19268d..784636ee --- a/testdata/foo.cwl +++ b/testdata/foo.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: v1.2 inputs: diff --git a/testdata/formattest2.cwl b/testdata/formattest2.cwl old mode 100644 new mode 100755 index 5e179949..4dcb7a18 --- a/testdata/formattest2.cwl +++ b/testdata/formattest2.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner $namespaces: edam: http://edamontology.org/ $schemas: diff --git a/testdata/formattest2_v1_0.cwl b/testdata/formattest2_v1_0.cwl old mode 100644 new mode 100755 index 3c330223..9df4402f --- a/testdata/formattest2_v1_0.cwl +++ b/testdata/formattest2_v1_0.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner $namespaces: edam: http://edamontology.org/ $schemas: diff --git a/testdata/formattest2_v1_1.cwl b/testdata/formattest2_v1_1.cwl old mode 100644 new mode 100755 index 30bb3901..0837da17 --- a/testdata/formattest2_v1_1.cwl +++ b/testdata/formattest2_v1_1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner $namespaces: edam: http://edamontology.org/ $schemas: diff --git a/testdata/js-expr-req-wf.cwl b/testdata/js-expr-req-wf.cwl old mode 100644 new mode 100755 index a54bd780..32c15db9 --- a/testdata/js-expr-req-wf.cwl +++ b/testdata/js-expr-req-wf.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.2 $graph: - id: tool @@ -27,4 +28,4 @@ $graph: tool: run: "#tool" in: {} - out: [out] \ No newline at end of file + out: [out] diff --git a/testdata/md5sum.cwl b/testdata/md5sum.cwl old mode 100644 new mode 100755 index 0c426a30..ca5454a6 --- a/testdata/md5sum.cwl +++ b/testdata/md5sum.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow diff --git a/testdata/md5sum_v11.cwl b/testdata/md5sum_v11.cwl old mode 100644 new mode 100755 index 3453b29c..b5877ddd --- a/testdata/md5sum_v11.cwl +++ b/testdata/md5sum_v11.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.1 class: Workflow diff --git a/testdata/md5sum_v12.cwl b/testdata/md5sum_v12.cwl old mode 100644 new mode 100755 index 2ade16f9..09fa7bb3 --- a/testdata/md5sum_v12.cwl +++ b/testdata/md5sum_v12.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner cwlVersion: v1.2 class: Workflow diff --git a/testdata/record-output-wf_v1_0.cwl b/testdata/record-output-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/record-output-wf_v1_1.cwl b/testdata/record-output-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/record-output-wf_v1_2.cwl b/testdata/record-output-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/record-output_v1_0.cwl b/testdata/record-output_v1_0.cwl old mode 100644 new mode 100755 index 13339856..b7771306 --- a/testdata/record-output_v1_0.cwl +++ b/testdata/record-output_v1_0.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: v1.0 hints: @@ -38,4 +39,4 @@ arguments: - {valueFrom: "> foo", position: 3, shellQuote: false} - {valueFrom: "&&", position: 4, shellQuote: false} - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} \ No newline at end of file + - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/testdata/record-output_v1_1.cwl b/testdata/record-output_v1_1.cwl old mode 100644 new mode 100755 index 84cd1771..e28f6ea9 --- a/testdata/record-output_v1_1.cwl +++ b/testdata/record-output_v1_1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: v1.1 requirements: @@ -35,4 +36,4 @@ arguments: - {valueFrom: "> foo", position: 3, shellQuote: false} - {valueFrom: "&&", position: 4, shellQuote: false} - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} \ No newline at end of file + - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/testdata/record-output_v1_2.cwl b/testdata/record-output_v1_2.cwl old mode 100644 new mode 100755 index 6f154cb2..d9f68778 --- a/testdata/record-output_v1_2.cwl +++ b/testdata/record-output_v1_2.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: CommandLineTool cwlVersion: v1.2 requirements: @@ -35,4 +36,4 @@ arguments: - {valueFrom: "> foo", position: 3, shellQuote: false} - {valueFrom: "&&", position: 4, shellQuote: false} - {valueFrom: "cat", position: 5} - - {valueFrom: "> bar", position: 7, shellQuote: false} \ No newline at end of file + - {valueFrom: "> bar", position: 7, shellQuote: false} diff --git a/testdata/remote-cwl/tool1.cwl b/testdata/remote-cwl/tool1.cwl old mode 100644 new mode 100755 index 38e0e1e3..64453b4c --- a/testdata/remote-cwl/tool1.cwl +++ b/testdata/remote-cwl/tool1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner # We have this tool to test both local and remote packing class: CommandLineTool diff --git a/testdata/remote-cwl/tool2.cwl b/testdata/remote-cwl/tool2.cwl old mode 100644 new mode 100755 index 66d20a09..b2c7c3ea --- a/testdata/remote-cwl/tool2.cwl +++ b/testdata/remote-cwl/tool2.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner # We have this tool to test both local and remote packing class: CommandLineTool diff --git a/testdata/remote-cwl/wf1.cwl b/testdata/remote-cwl/wf1.cwl old mode 100644 new mode 100755 index eaa286c0..bd08a511 --- a/testdata/remote-cwl/wf1.cwl +++ b/testdata/remote-cwl/wf1.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 inputs: @@ -24,4 +25,4 @@ outputs: requirements: SchemaDefRequirement: types: - - $import: ../types/testtypes.yml \ No newline at end of file + - $import: ../types/testtypes.yml diff --git a/testdata/revsort-run-1-packed.cwl b/testdata/revsort-run-1-packed.cwl old mode 100644 new mode 100755 index 251587da..a8d96664 --- a/testdata/revsort-run-1-packed.cwl +++ b/testdata/revsort-run-1-packed.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner { "$graph": [ { @@ -134,4 +135,4 @@ "file:///home/stain/src/cwltool/tests/wf/empty.ttl", "file:///home/stain/src/cwltool/tests/wf/empty2.ttl" ] -} \ No newline at end of file +} diff --git a/testdata/scatter-wf1_v1_0.cwl b/testdata/scatter-wf1_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf1_v1_1.cwl b/testdata/scatter-wf1_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf1_v1_2.cwl b/testdata/scatter-wf1_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf2_v1_0.cwl b/testdata/scatter-wf2_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf2_v1_1.cwl b/testdata/scatter-wf2_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf2_v1_2.cwl b/testdata/scatter-wf2_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf3_v1_0.cwl b/testdata/scatter-wf3_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf3_v1_1.cwl b/testdata/scatter-wf3_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/scatter-wf3_v1_2.cwl b/testdata/scatter-wf3_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom2-wf_v1_0.cwl b/testdata/step-valuefrom2-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom2-wf_v1_1.cwl b/testdata/step-valuefrom2-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom2-wf_v1_2.cwl b/testdata/step-valuefrom2-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom3-wf_v1_0.cwl b/testdata/step-valuefrom3-wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom3-wf_v1_1.cwl b/testdata/step-valuefrom3-wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/step-valuefrom3-wf_v1_2.cwl b/testdata/step-valuefrom3-wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_v1_0.cwl b/testdata/step_valuefrom5_wf_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_v1_1.cwl b/testdata/step_valuefrom5_wf_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_v1_2.cwl b/testdata/step_valuefrom5_wf_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_with_id_v1_0.cwl b/testdata/step_valuefrom5_wf_with_id_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_with_id_v1_1.cwl b/testdata/step_valuefrom5_wf_with_id_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/step_valuefrom5_wf_with_id_v1_2.cwl b/testdata/step_valuefrom5_wf_with_id_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/wc3-tool_v1_0.cwl b/testdata/wc3-tool_v1_0.cwl old mode 100644 new mode 100755 diff --git a/testdata/wc3-tool_v1_1.cwl b/testdata/wc3-tool_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/wc3-tool_v1_2.cwl b/testdata/wc3-tool_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/wf2.cwl b/testdata/wf2.cwl old mode 100644 new mode 100755 index 6b3145a1..1ef89e9d --- a/testdata/wf2.cwl +++ b/testdata/wf2.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 inputs: @@ -26,4 +27,4 @@ outputs: requirements: SchemaDefRequirement: types: - - $import: types/testtypes.yml \ No newline at end of file + - $import: types/testtypes.yml diff --git a/testdata/workflow_input_format_expr.cwl b/testdata/workflow_input_format_expr.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_format_expr_v1_1.cwl b/testdata/workflow_input_format_expr_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_format_expr_v1_2.cwl b/testdata/workflow_input_format_expr_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr.cwl b/testdata/workflow_input_sf_expr.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr_array.cwl b/testdata/workflow_input_sf_expr_array.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr_array_v1_1.cwl b/testdata/workflow_input_sf_expr_array_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr_array_v1_2.cwl b/testdata/workflow_input_sf_expr_array_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr_v1_1.cwl b/testdata/workflow_input_sf_expr_v1_1.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflow_input_sf_expr_v1_2.cwl b/testdata/workflow_input_sf_expr_v1_2.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflows/count-lines16-wf.cwl b/testdata/workflows/count-lines16-wf.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflows/import-in-type.cwl b/testdata/workflows/import-in-type.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflows/scatter-wf4.cwl b/testdata/workflows/scatter-wf4.cwl old mode 100644 new mode 100755 diff --git a/testdata/workflows/wf5.cwl b/testdata/workflows/wf5.cwl old mode 100644 new mode 100755 index d547bb90..382e68db --- a/testdata/workflows/wf5.cwl +++ b/testdata/workflows/wf5.cwl @@ -1,3 +1,4 @@ +#!/usr/bin/env cwl-runner # Checks symbolic links on github class: Workflow