Skip to content

Instantly share code, notes, and snippets.

@stain
Created March 10, 2017 14:52
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save stain/1b73331d855cbad8882008d677d6c440 to your computer and use it in GitHub Desktop.
Save stain/1b73331d855cbad8882008d677d6c440 to your computer and use it in GitHub Desktop.
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
$graph:
- id: echocmd
class: CommandLineTool
inputs:
echo-in:
type: string
label: "Message"
doc: "The message to print"
default: "Hello World"
inputBinding: {}
outputs:
echo-out:
type: stdout
label: "Printed Message"
doc: "The file containing the message"
baseCommand: echo
stdout: messageout.txt
- id: main
class: Workflow
label: "Hello World"
doc: "Puts a message into a file using echo"
inputs: []
outputs:
output:
type: File
outputSource: step0/echo-out
steps:
step0:
run: "#echocmd"
in: []
out: [echo-out]
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix CommandLineTool: <https://w3id.org/cwl/cwl#CommandLineTool/> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix EnvVarRequirement: <https://w3id.org/cwl/cwl#EnvVarRequirement/> .
@prefix EnvironmentDef: <https://w3id.org/cwl/cwl#EnvironmentDef/> .
@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .
@prefix File: <https://w3id.org/cwl/cwl#File/> .
@prefix InlineJavascriptRequirement: <https://w3id.org/cwl/cwl#InlineJavascriptRequirement/> .
@prefix LinkMergeMethod: <https://w3id.org/cwl/cwl#LinkMergeMethod/> .
@prefix Parameter: <https://w3id.org/cwl/cwl#Parameter/> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@prefix ScatterMethod: <https://w3id.org/cwl/cwl#ScatterMethod/> .
@prefix SchemaDefRequirement: <https://w3id.org/cwl/cwl#SchemaDefRequirement/> .
@prefix SoftwarePackage: <https://w3id.org/cwl/cwl#SoftwarePackage/> .
@prefix SoftwareRequirement: <https://w3id.org/cwl/cwl#SoftwareRequirement/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix cwl: <https://w3id.org/cwl/cwl#> .
@prefix ns1: <rdfs:> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sld: <https://w3id.org/cwl/salad#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main> a cwl:Workflow ;
Workflow:steps <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/step0> ;
cwl:outputs <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/output> ;
ns1:comment "Puts a message into a file using echo" ;
ns1:label "Hello World" .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd> a cwl:CommandLineTool ;
cwl:baseCommand ( "echo" ) ;
cwl:inputs <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd/echo-in> ;
cwl:outputs <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd/echo-out> ;
cwl:stdout "messageout.txt" .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd/echo-in> cwl:default "Hello World" ;
cwl:inputBinding [ ] ;
sld:type xsd:string ;
ns1:comment "The message to print" ;
ns1:label "Message" .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd/echo-out> cwl:outputBinding [ CommandOutputBinding:glob "messageout.txt" ] ;
sld:type cwl:File ;
ns1:comment "The file containing the message" ;
ns1:label "Printed Message" .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/output> cwl:outputSource <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/step0/echo-out> ;
sld:type cwl:File .
<https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/step0> cwl:out <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#main/step0/echo-out> ;
cwl:run <https://raw.githubusercontent.com/common-workflow-language/workflows/master/workflows/hello/hello.cwl#echocmd> .
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment