Revert cwltool in shebang

kinow · mr-c · commit 28c7baae39c3 · 2022-09-20T16:12:10.000+02:00
diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/src/_includes/cwl/environment-variables/env.cwl b/src/_includes/cwl/environment-variables/env.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/expressions/expression.cwl b/src/_includes/cwl/expressions/expression.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/true_shebang.cwl b/src/_includes/cwl/true_shebang.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.2
 class: CommandLineTool
diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/workflows/1st-workflow.cwl b/src/_includes/cwl/workflows/1st-workflow.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: Workflow
diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/workflows/nestedworkflows.cwl b/src/_includes/cwl/workflows/nestedworkflows.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: Workflow
diff --git a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: Workflow
diff --git a/src/_includes/cwl/workflows/scatter-two-steps.cwl b/src/_includes/cwl/workflows/scatter-two-steps.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: Workflow
diff --git a/src/_includes/cwl/workflows/scatter-workflow.cwl b/src/_includes/cwl/workflows/scatter-workflow.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: Workflow
diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl
@@ -1,4 +1,4 @@
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 
 cwlVersion: v1.0
 class: CommandLineTool
diff --git a/src/faq.md b/src/faq.md
@@ -87,7 +87,7 @@ Below is an example workaround for this,
 pending a more sophisticated fix.
 
 ```yaml
-#!/usr/bin/env cwltool
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-#!/usr/bin/env cwltool`
	`1`	`+#!/usr/bin/env cwl-runner`
`2`	`2`
`3`	`3`	`cwlVersion: v1.0`
`4`	`4`	`class: CommandLineTool`