s/cwl-runner/cwltool (where appropriate)

kinow · mr-c · commit 854be17f891a · 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner 
+#!/usr/bin/env cwltool
 cwlVersion: v1.0
 class: CommandLineTool
 
@@ -43,7 +43,7 @@ inputs:
 baseCommand: [ biom, convert ]
 
 arguments:
-  - valueFrom: $(inputs.biom.nameroot).hdf5  
+  - valueFrom: $(inputs.biom.nameroot).hdf5
     prefix: --output-fp
   - --to-hdf5
 
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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 cwlVersion: v1.0
 class: CommandLineTool
 
@@ -38,7 +38,7 @@ s:contributor:
 s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
 s:dateCreated: "2016-12-13"
-s:license: https://spdx.org/licenses/Apache-2.0 
+s:license: https://spdx.org/licenses/Apache-2.0
 
 $namespaces:
   s: https://schema.org/
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 cwl-runner
+#!/usr/bin/env cwltool
 cwlVersion: v1.0
 class: CommandLineTool
 
@@ -42,7 +42,7 @@ s:contributor:
 s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
 s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
 s:dateCreated: "2016-12-13"
-s:license: https://spdx.org/licenses/Apache-2.0 
+s:license: https://spdx.org/licenses/Apache-2.0
 
 s:keywords: edam:topic_0091 , edam:topic_0622
 s:programmingLanguage: C
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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 cwlVersion: v1.0
 class: CommandLineTool
@@ -8,6 +8,6 @@ inputs:
     type: string
     inputBinding:
       position: 1
-outputs: 
+outputs:
   echo_out:
     type: stdout
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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 cwlVersion: v1.0
 class: Workflow
@@ -8,13 +8,13 @@ requirements:
  SubworkflowFeatureRequirement: {}
 
 inputs:
-  message_array: string[] 
+  message_array: string[]
 
 steps:
   subworkflow:
-    run: 
+    run:
       class: Workflow
-      inputs: 
+      inputs:
         message: string
       outputs: []
       steps:
@@ -29,7 +29,7 @@ steps:
             input_file: echo/echo_out
           out: []
     scatter: message
-    in: 
+    in:
       message: message_array
     out: []
 outputs: []
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 cwl-runner
+#!/usr/bin/env cwltool
 
 cwlVersion: v1.0
 class: Workflow
@@ -7,7 +7,7 @@ requirements:
  ScatterFeatureRequirement: {}
 
 inputs:
-  message_array: string[] 
+  message_array: string[]
 
 steps:
   echo:
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 cwl-runner
+#!/usr/bin/env cwltool
 
 cwlVersion: v1.0
 class: Workflow
@@ -7,7 +7,7 @@ requirements:
   ScatterFeatureRequirement: {}
 
 inputs:
-  message_array: string[] 
+  message_array: string[]
 
 steps:
   echo:
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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 
 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 cwl-runner
+#!/usr/bin/env cwltool
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/src/topics/additional-arguments-and-parameters.md b/src/topics/additional-arguments-and-parameters.md
@@ -27,9 +27,9 @@ Next, create a sample Java file to use with the command-line tool.
 $ echo "public class Hello {}" > Hello.java
 ```
 
-And now invoke `cwl-runner` providing the tool description and the input object on the command line:
+And now invoke `cwltool` providing the tool description and the input object on the command line:
 
-```{runcmd} cwl-runner arguments.cwl arguments-job.yml
+```{runcmd} cwltool arguments.cwl arguments-job.yml
 :working-directory: src/_includes/cwl/additional-arguments-and-parameters
 ```
 
diff --git a/src/topics/creating-files-at-runtime.md b/src/topics/creating-files-at-runtime.md
@@ -51,10 +51,10 @@ which is YAML quoting syntax, and means that you are using a multiline string
 See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting.
 ```
 
-Now invoke `cwl-runner` with the tool description and the input object on the
+Now invoke `cwltool` with the tool description and the input object on the
 command line:
 
-```{runcmd} cwl-runner createfile.cwl echo-job.yml
+```{runcmd} cwltool createfile.cwl echo-job.yml
 :working-directory: src/_includes/cwl/creating-files-at-runtime/
 ```
 
diff --git a/src/topics/environment-variables.md b/src/topics/environment-variables.md
@@ -15,10 +15,10 @@ the tool using `EnvVarRequirement`.
 :caption: "`echo-job.yml`"
 ```
 
-Now invoke `cwl-runner` with the tool description and the input object on the
+Now invoke `cwltool` with the tool description and the input object on the
 command line:
 
-```{runcmd} cwl-runner env.cwl echo-job.yml
+```{runcmd} cwltool env.cwl echo-job.yml
 :working-directory: src/_includes/cwl/environment-variables/
 ```
 
diff --git a/src/topics/expressions.md b/src/topics/expressions.md
@@ -33,7 +33,7 @@ represented simply by a set of empty brackets.
 
 We can then run `expression.cwl`:
 
-```{runcmd} cwl-runner expression.cwl empty.yml
+```{runcmd} cwltool expression.cwl empty.yml
 :name: running-expression.cwl
 :caption: Running `expression.cwl`
 :working-directory: src/_includes/cwl/expressions/
diff --git a/src/topics/file-formats.md b/src/topics/file-formats.md
@@ -49,7 +49,7 @@ ___Note:___ To follow the example below, you need to download the example input
 $ wget https://github.com/common-workflow-language/user_guide/raw/main/_includes/cwl/file-formats/file-formats.bam
 ```
 
-Now invoke `cwl-runner` with the tool description and the input object on the
+Now invoke `cwltool` with the tool description and the input object on the
 command line:
 
 ```{runcmd} cwltool metadata_example.cwl sample.yml
diff --git a/src/topics/inputs.md b/src/topics/inputs.md
@@ -38,11 +38,11 @@ Next, create a whale.txt using [touch] by typing `touch whale.txt` on the comman
 $ touch whale.txt
 ```
 
-Now invoke `cwl-runner` with the tool description and the input object on the command line,
-using the command `cwl-runner inp.cwl inp-job.yml`. The following boxed text describes these
+Now invoke `cwltool` with the tool description and the input object on the command line,
+using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these
 two commands and the expected output from the command line:
 
-```{runcmd} cwl-runner inp.cwl inp-job.yml
+```{runcmd} cwltool inp.cwl inp-job.yml
 :working-directory: src/_includes/cwl/inputs
 ````
 
@@ -151,10 +151,10 @@ the type name to indicate that input parameter is array of that type.
 :name: array-inputs-job.yml
 ```
 
-Now invoke `cwl-runner` providing the tool description and the input object
+Now invoke `cwltool` providing the tool description and the input object
 on the command line:
 
-```{runcmd} cwl-runner array-inputs.cwl array-inputs-job.yml
+```{runcmd} cwltool array-inputs.cwl array-inputs-job.yml
 :working-directory: src/_includes/cwl/inputs/
 ```
 
@@ -195,7 +195,7 @@ parameters together to describe these two conditions.
 :name: record-job1.yml
 ```
 
-```{runcmd} cwl-runner record.cwl record-job1.yml
+```{runcmd} cwltool record.cwl record-job1.yml
 :working-directory: src/_includes/cwl/inputs/
 ```
 
@@ -207,7 +207,7 @@ In the first example, you can't provide `itemA` without also providing `itemB`.
 :name: record-job2.yml
 ```
 
-```{runcmd} cwl-runner record.cwl record-job2.yml
+```{runcmd} cwltool record.cwl record-job2.yml
 :working-directory: src/_includes/cwl/inputs
 ````
 
@@ -225,7 +225,7 @@ is added to the command line and `itemD` is ignored.
 :name: record-job3.yml
 ```
 
-```{runcmd} cwl-runner record.cwl record-job3.yml
+```{runcmd} cwltool record.cwl record-job3.yml
 :working-directory: src/_includes/cwl/inputs
 ````
 
diff --git a/src/topics/outputs.md b/src/topics/outputs.md
@@ -42,9 +42,9 @@ $ touch hello.txt && tar -cvf hello.tar hello.txt
 hello.txt
 ```
 
-And now invoke `cwl-runner` with the tool description and the input object on the command line:
+And now invoke `cwltool` with the tool description and the input object on the command line:
 
-```{runcmd} cwl-runner tar.cwl tar-job.yml
+```{runcmd} cwltool tar.cwl tar-job.yml
 :working-directory: src/_includes/cwl/outputs/
 ```
 
@@ -79,10 +79,10 @@ stdout` on the corresponding output parameter.
 :caption: "`echo-job.yml`"
 ```
 
-Now invoke `cwl-runner` providing the tool description and the input object
+Now invoke `cwltool` providing the tool description and the input object
 on the command line:
 
-```{runcmd} cwl-runner stdout.cwl echo-job.yml
+```{runcmd} cwltool stdout.cwl echo-job.yml
 :working-directory: src/_includes/cwl/outputs/
 ```
 
@@ -102,10 +102,10 @@ You can also capture multiple output files into an array of files using `glob`.
 :name: array-outputs-job.yml
 ```
 
-Now invoke `cwl-runner` providing the tool description and the input object
+Now invoke `cwltool` providing the tool description and the input object
 on the command line:
 
-```{runcmd} cwl-runner array-outputs.cwl array-outputs-job.yml
+```{runcmd} cwltool array-outputs.cwl array-outputs-job.yml
 :working-directory: src/_includes/cwl/outputs/
 ```
 
diff --git a/src/topics/parameter-references.md b/src/topics/parameter-references.md
diff --git a/src/topics/staging-input-files.md b/src/topics/staging-input-files.md
diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md
diff --git a/src/topics/workflows.md b/src/topics/workflows.md

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