Commit 96008751 authored by Tammo Jan Dijkema's avatar Tammo Jan Dijkema

Add CWL testing files

parent 4ffefae4
Pipeline #140 failed with stages
in 1 minute and 52 seconds
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
inputs:
message:
type: string
inputBinding:
position: 1
outputs:
- id: echo_out
type: stdout
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: cat
baseCommand:
- cat
inputs:
- id: files
type:
- File
- type: array
items: File
inputBinding:
position: 0
outputs:
- id: output
type: stdout
label: cat
message_array:
- Hello world!
- Hola mundo!
- Bonjour le monde!
- Hallo welt!
class: Workflow
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: message_array
type: 'string[]'
'sbg:x': -62
'sbg:y': 97
outputs:
- id: output
outputSource:
- cat/output
type: File
'sbg:x': 549
'sbg:y': 14
- id: output_1
outputSource:
- cat_1/output
type: File
'sbg:x': 626.203125
'sbg:y': 204
steps:
- id: echo
in:
- id: message
source: message_array
out:
- id: echo_out
run: 1st-tool.cwl
scatter:
- message
'sbg:x': 173
'sbg:y': -17
- id: cat
in:
- id: files
source:
- echo/echo_out
out:
- id: output
run: ./cat.cwl
label: cat
'sbg:x': 378.203125
'sbg:y': 21.5
- id: 1st_tool
in:
- id: message
source: message_array
out:
- id: echo_out
run: ./1st-tool.cwl
scatter:
- message
'sbg:x': 176.203125
'sbg:y': 231.5
- id: cat_1
in:
- id: files
source:
- 1st_tool/echo_out
out:
- id: output
run: ./cat.cwl
label: cat
'sbg:x': 454.203125
'sbg:y': 219
requirements:
- class: ScatterFeatureRequirement
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: scattertest
label: scattertest
class: Workflow
cwlVersion: v1.0
inputs: []
outputs: []
steps: []
doc: ''
class: Workflow
cwlVersion: v1.0
id: two_files
label: two_files
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: message
type: string
'sbg:x': -327.3938293457031
'sbg:y': -142
- id: message_1
type: string
'sbg:x': -332.8984375
'sbg:y': 94
outputs:
- id: echo_out
outputSource: combine/out_files
type: 'File[]'
'sbg:x': 112
'sbg:y': -88
steps:
- id: 1st_tool
in:
- id: message
source: message
out:
- id: echo_out
run: ./1st-tool.cwl
'sbg:x': -88
'sbg:y': -185
- id: 1st_tool_1
in:
- id: message
source: message_1
out:
- id: echo_out
run: ./1st-tool.cwl
'sbg:x': -89
'sbg:y': -27
- id: combine
in:
input_file:
source:
- 1st_tool_1/echo_out
- 1st_tool/echo_out
out:
- id: out_files
run:
class: ExpressionTool
inputs:
input_file:
type: File[]
outputs:
out_files:
type: File[]
expression: |
${
var output = []
for(var index in inputs.input_file){
var current_file = inputs.input_file[index]
current_file.basename = 'output_' + index
output.push(current_file)
}
return {out_files: output}
}
requirements:
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
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