add cwl-runner header to all CWL test files, mark them executable

common-workflow-language · Oct 23, 2024 · 086a4ab · 086a4ab
1 parent ad21f9a
commit 086a4ab
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Showing 79 changed files with 36 additions and 11 deletions.
diff --git 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
@@ -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: {}
+  InlineJavascriptRequirement: {}
diff --git 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: {}
+  InlineJavascriptRequirement: {}
diff --git 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
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.2
 inputs:
@@ -31,4 +32,4 @@ outputs:
 
 requirements:
   InlineJavascriptRequirement: {}
-  MultipleInputFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
diff --git 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: {}
+  MultipleInputFeatureRequirement: {}
diff --git a/testdata/count-lines6-single-source-wf_v1_0.cwl b/testdata/count-lines6-single-source-wf_v1_0.cwl
diff --git a/testdata/count-lines6-single-source-wf_v1_1.cwl b/testdata/count-lines6-single-source-wf_v1_1.cwl
diff --git a/testdata/count-lines6-single-source-wf_v1_2.cwl b/testdata/count-lines6-single-source-wf_v1_2.cwl
diff --git a/testdata/count-lines6-wf_v1_0.cwl b/testdata/count-lines6-wf_v1_0.cwl
diff --git a/testdata/count-lines6-wf_v1_1.cwl b/testdata/count-lines6-wf_v1_1.cwl
diff --git a/testdata/count-lines6-wf_v1_2.cwl b/testdata/count-lines6-wf_v1_2.cwl
diff --git a/testdata/count-lines7-single-source-wf_v1_0.cwl b/testdata/count-lines7-single-source-wf_v1_0.cwl
diff --git a/testdata/count-lines7-single-source-wf_v1_1.cwl b/testdata/count-lines7-single-source-wf_v1_1.cwl
diff --git a/testdata/count-lines7-single-source-wf_v1_2.cwl b/testdata/count-lines7-single-source-wf_v1_2.cwl
diff --git a/testdata/count-lines7-wf_v1_0.cwl b/testdata/count-lines7-wf_v1_0.cwl
diff --git a/testdata/count-lines7-wf_v1_1.cwl b/testdata/count-lines7-wf_v1_1.cwl
diff --git a/testdata/count-lines7-wf_v1_2.cwl b/testdata/count-lines7-wf_v1_2.cwl
diff --git a/testdata/dockstore-tool-md5sum.cwl b/testdata/dockstore-tool-md5sum.cwl
diff --git a/testdata/dockstore-tool-md5sum_v11.cwl b/testdata/dockstore-tool-md5sum_v11.cwl
diff --git a/testdata/dockstore-tool-md5sum_v12.cwl b/testdata/dockstore-tool-md5sum_v12.cwl
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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]
+        out: [out]
diff --git 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
@@ -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
@@ -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
diff --git a/testdata/record-output-wf_v1_1.cwl b/testdata/record-output-wf_v1_1.cwl
diff --git a/testdata/record-output-wf_v1_2.cwl b/testdata/record-output-wf_v1_2.cwl
diff --git 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}
+  - {valueFrom: "> bar", position: 7, shellQuote: false}
diff --git 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}
+  - {valueFrom: "> bar", position: 7, shellQuote: false}
diff --git 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}
+  - {valueFrom: "> bar", position: 7, shellQuote: false}
diff --git 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
@@ -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
@@ -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
+      - $import: ../types/testtypes.yml
diff --git a/testdata/revsort-run-1-packed.cwl b/testdata/revsort-run-1-packed.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
     "$graph": [
         {
@@ -134,4 +135,4 @@
         "file:///home/stain/src/cwltool/tests/wf/empty.ttl",
         "file:///home/stain/src/cwltool/tests/wf/empty2.ttl"
     ]
-}
+}
diff --git a/testdata/scatter-wf1_v1_0.cwl b/testdata/scatter-wf1_v1_0.cwl
diff --git a/testdata/scatter-wf1_v1_1.cwl b/testdata/scatter-wf1_v1_1.cwl
diff --git a/testdata/scatter-wf1_v1_2.cwl b/testdata/scatter-wf1_v1_2.cwl
diff --git a/testdata/scatter-wf2_v1_0.cwl b/testdata/scatter-wf2_v1_0.cwl
diff --git a/testdata/scatter-wf2_v1_1.cwl b/testdata/scatter-wf2_v1_1.cwl
diff --git a/testdata/scatter-wf2_v1_2.cwl b/testdata/scatter-wf2_v1_2.cwl
diff --git a/testdata/scatter-wf3_v1_0.cwl b/testdata/scatter-wf3_v1_0.cwl
diff --git a/testdata/scatter-wf3_v1_1.cwl b/testdata/scatter-wf3_v1_1.cwl
diff --git a/testdata/scatter-wf3_v1_2.cwl b/testdata/scatter-wf3_v1_2.cwl
diff --git a/testdata/step-valuefrom2-wf_v1_0.cwl b/testdata/step-valuefrom2-wf_v1_0.cwl
diff --git a/testdata/step-valuefrom2-wf_v1_1.cwl b/testdata/step-valuefrom2-wf_v1_1.cwl
diff --git a/testdata/step-valuefrom2-wf_v1_2.cwl b/testdata/step-valuefrom2-wf_v1_2.cwl
diff --git a/testdata/step-valuefrom3-wf_v1_0.cwl b/testdata/step-valuefrom3-wf_v1_0.cwl
diff --git a/testdata/step-valuefrom3-wf_v1_1.cwl b/testdata/step-valuefrom3-wf_v1_1.cwl
diff --git a/testdata/step-valuefrom3-wf_v1_2.cwl b/testdata/step-valuefrom3-wf_v1_2.cwl
diff --git a/testdata/step_valuefrom5_wf_v1_0.cwl b/testdata/step_valuefrom5_wf_v1_0.cwl
diff --git a/testdata/step_valuefrom5_wf_v1_1.cwl b/testdata/step_valuefrom5_wf_v1_1.cwl
diff --git a/testdata/step_valuefrom5_wf_v1_2.cwl b/testdata/step_valuefrom5_wf_v1_2.cwl
diff --git a/testdata/step_valuefrom5_wf_with_id_v1_0.cwl b/testdata/step_valuefrom5_wf_with_id_v1_0.cwl
diff --git a/testdata/step_valuefrom5_wf_with_id_v1_1.cwl b/testdata/step_valuefrom5_wf_with_id_v1_1.cwl
diff --git a/testdata/step_valuefrom5_wf_with_id_v1_2.cwl b/testdata/step_valuefrom5_wf_with_id_v1_2.cwl
diff --git a/testdata/wc3-tool_v1_0.cwl b/testdata/wc3-tool_v1_0.cwl
diff --git a/testdata/wc3-tool_v1_1.cwl b/testdata/wc3-tool_v1_1.cwl
diff --git a/testdata/wc3-tool_v1_2.cwl b/testdata/wc3-tool_v1_2.cwl
diff --git 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
+      - $import: types/testtypes.yml
diff --git a/testdata/workflow_input_format_expr.cwl b/testdata/workflow_input_format_expr.cwl
diff --git a/testdata/workflow_input_format_expr_v1_1.cwl b/testdata/workflow_input_format_expr_v1_1.cwl
diff --git a/testdata/workflow_input_format_expr_v1_2.cwl b/testdata/workflow_input_format_expr_v1_2.cwl
diff --git a/testdata/workflow_input_sf_expr.cwl b/testdata/workflow_input_sf_expr.cwl
diff --git a/testdata/workflow_input_sf_expr_array.cwl b/testdata/workflow_input_sf_expr_array.cwl
diff --git a/testdata/workflow_input_sf_expr_array_v1_1.cwl b/testdata/workflow_input_sf_expr_array_v1_1.cwl
diff --git a/testdata/workflow_input_sf_expr_array_v1_2.cwl b/testdata/workflow_input_sf_expr_array_v1_2.cwl
diff --git a/testdata/workflow_input_sf_expr_v1_1.cwl b/testdata/workflow_input_sf_expr_v1_1.cwl
diff --git a/testdata/workflow_input_sf_expr_v1_2.cwl b/testdata/workflow_input_sf_expr_v1_2.cwl
diff --git a/testdata/workflows/count-lines16-wf.cwl b/testdata/workflows/count-lines16-wf.cwl
diff --git a/testdata/workflows/import-in-type.cwl b/testdata/workflows/import-in-type.cwl
diff --git a/testdata/workflows/scatter-wf4.cwl b/testdata/workflows/scatter-wf4.cwl
diff --git 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