-
-
Notifications
You must be signed in to change notification settings - Fork 17
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
expr refactor: quoting in generated javascript is sometimes wrong #46
Comments
One example is https://github.com/mvdbeek/galaxy/blob/debug_stuff/test/unit/tools/cwl_tools/v1.0/v1.0/count-lines11-null-step-wf-noET.cwl, which results in #!/usr/bin/env cwl-runner
class: Workflow
id: file:///Users/mvandenb/src/galaxy/test/functional/tools/cwl_tools/v1.0/v1.0/count-lines11-null-step-wf-noET.cwl
inputs: []
outputs:
- id: wc_output
outputSource: step1/output
type: File
cwlVersion: v1.0
steps:
- id: step0
in: []
out:
- output
run:
class: CommandLineTool
id: null-expression3-tool.cwl
inputs: []
outputs:
- id: output
type: Any
requirements:
- class: InitialWorkDirRequirement
listing:
- entryname: expression.js
entry: |-
"use strict";
var inputs=$/(inputs);
var runtime=$/(runtime);
var ret = function(){{'output': null }}();
process.stdout.write(JSON.stringify(ret));
hints:
- class: DockerRequirement
dockerPull: node:slim
- class: SoftwareRequirement
packages:
- package: nodejs
cwlVersion: v1.0
baseCommand:
- nodejs
- expression.js
stdout: cwl.output.json
- id: step1
in:
- id: file1
source: step0/output
default:
class: File
location: whale.txt
out:
- output
run:
class: CommandLineTool
id: wc-tool.cwl
inputs:
- id: file1
type: File
outputs:
- id: output
outputBinding:
glob: output
type: File
hints:
- ramMin: 8
class: ResourceRequirement
cwlVersion: v1.0
baseCommand:
- wc
- -l
stdin: $(inputs.file1.path)
stdout: output This is for cwl-utils updated this morning from the master branch. |
Thanks for this! Found an error in a CWL conformance test and cwltool! common-workflow-language/cwltool#1369 |
I've tried #47 with #916 and it doesn't look quite right ? #!/usr/bin/env cwl-runner
class: Workflow
id: file:///Users/mvandenb/src/galaxy/test/functional/tools/cwl_tools/v1.0/v1.0/count-lines11-null-step-wf-noET.cwl
inputs: []
outputs:
- id: wc_output
outputSource: step1/output
type: File
cwlVersion: v1.0
steps:
- id: step0
in: []
out:
- output
run:
class: CommandLineTool
id: null-expression3-tool.cwl
inputs: []
outputs:
- id: output
type:
- 'null'
- Any
requirements:
- class: InitialWorkDirRequirement
listing:
- entryname: expression.js
entry: |-
"use strict";
var inputs=$/(inputs);
var runtime=$/(runtime);
var ret = function(){{'output': null }}();
process.stdout.write(JSON.stringify(ret));
hints:
- class: DockerRequirement
dockerPull: node:slim
- class: SoftwareRequirement
packages:
- package: nodejs
cwlVersion: v1.0
baseCommand:
- nodejs
- expression.js
stdout: cwl.output.json
- id: step1
in:
- id: file1
source: step0/output
default:
class: File
location: whale.txt
out:
- output
run:
class: CommandLineTool
id: wc-tool.cwl
inputs:
- id: file1
type: File
outputs:
- id: output
outputBinding:
glob: output
type: File
hints:
- ramMin: 8
class: ResourceRequirement
cwlVersion: v1.0
baseCommand:
- wc
- -l
stdin: $(inputs.file1.path)
stdout: output
|
OK, used the wrong tool ... sorry. |
@mvdbeek to provide a specific example
The text was updated successfully, but these errors were encountered: