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Add DeepHealth tissue/tumor prediction pipeline example #2

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Feb 17, 2022
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Add DeepHealth tissue/tumor prediction pipeline example #2

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1 change: 1 addition & 0 deletions docs/examples/draft/ml-predict-pipeline/index.html
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ro-crate-preview.html
382 changes: 382 additions & 0 deletions docs/examples/draft/ml-predict-pipeline/predictions.cwl
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class: Workflow
cwlVersion: v1.2
http://commonwl.org/cwltool#original_cwlVersion: v1.1
id: file:///cwl/predictions.cwl
inputs:
- id: file:///cwl/predictions.cwl#gpu
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#mode
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#slide
type: File
- id: file:///cwl/predictions.cwl#tissue-high-batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tissue-high-chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tissue-high-filter
type: string
- id: file:///cwl/predictions.cwl#tissue-high-label
type: string
- id: file:///cwl/predictions.cwl#tissue-high-level
type: int
- id: file:///cwl/predictions.cwl#tissue-low-batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tissue-low-chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tissue-low-label
type: string
- id: file:///cwl/predictions.cwl#tissue-low-level
type: int
- id: file:///cwl/predictions.cwl#tumor-batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tumor-chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#tumor-filter
type: string
- id: file:///cwl/predictions.cwl#tumor-label
type: string
- id: file:///cwl/predictions.cwl#tumor-level
type: int
outputs:
- id: file:///cwl/predictions.cwl#tissue
outputSource: file:///cwl/predictions.cwl#extract-tissue-high/tissue
type: File
- id: file:///cwl/predictions.cwl#tumor
outputSource: file:///cwl/predictions.cwl#classify-tumor/tumor
type: File
steps:
- id: file:///cwl/predictions.cwl#classify-tumor
in:
- id: file:///cwl/predictions.cwl#classify-tumor/batch
source: file:///cwl/predictions.cwl#tumor-batch
- id: file:///cwl/predictions.cwl#classify-tumor/chunk
source: file:///cwl/predictions.cwl#tumor-chunk
- id: file:///cwl/predictions.cwl#classify-tumor/filter
source: file:///cwl/predictions.cwl#tumor-filter
- id: file:///cwl/predictions.cwl#classify-tumor/filter_slide
source: file:///cwl/predictions.cwl#extract-tissue-low/tissue
- id: file:///cwl/predictions.cwl#classify-tumor/gpu
source: file:///cwl/predictions.cwl#gpu
- id: file:///cwl/predictions.cwl#classify-tumor/label
source: file:///cwl/predictions.cwl#tumor-label
- id: file:///cwl/predictions.cwl#classify-tumor/level
source: file:///cwl/predictions.cwl#tumor-level
- id: file:///cwl/predictions.cwl#classify-tumor/mode
source: file:///cwl/predictions.cwl#mode
- id: file:///cwl/predictions.cwl#classify-tumor/src
source: file:///cwl/predictions.cwl#unzip/mrxs
out:
- file:///cwl/predictions.cwl#classify-tumor/tumor
run:
arguments:
- -o
- $(runtime.outdir)
- --writer
- zip
class: CommandLineTool
cwlVersion: v1.1
id: _:5721fb1b-b8d0-418a-a28d-05c75550a565
inputs:
- id: file:///cwl/predictions.cwl#classify-tumor/run/batch
inputBinding:
prefix: --batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#classify-tumor/run/chunk
inputBinding:
prefix: --chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#classify-tumor/run/filter
inputBinding:
prefix: -F
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#classify-tumor/run/filter_slide
inputBinding:
prefix: --filter-slide
type:
- 'null'
- File
- id: file:///cwl/predictions.cwl#classify-tumor/run/gpu
inputBinding:
prefix: --gpu
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#classify-tumor/run/label
inputBinding:
prefix: -f
type: string
- id: file:///cwl/predictions.cwl#classify-tumor/run/level
inputBinding:
prefix: -l
type: int
- id: file:///cwl/predictions.cwl#classify-tumor/run/mode
inputBinding:
prefix: --mode
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#classify-tumor/run/src
inputBinding:
position: 1
secondaryFiles:
- pattern: "${\n if (self.nameext == '.mrxs') {\n return {\n class: \"\
File\",\n location: self.location.match(/.*\\//)[0] + \"/\" + self.nameroot,\n\
\ basename: self.nameroot};\n }\n else return null;\n}"
required: false
type: File
outputs:
- id: file:///cwl/predictions.cwl#classify-tumor/run/tumor
outputBinding:
glob: $(inputs.src.basename).zip
outputEval: ${self[0].basename=inputs.label + '.zip'; return self;}
type: File
requirements:
- class: DockerRequirement
dockerPull: slaid:0.60.4-develop-tumor_model-level_1
- class: InitialWorkDirRequirement
listing:
- $(inputs.src)
- class: InlineJavascriptRequirement
- id: file:///cwl/predictions.cwl#extract-tissue-high
in:
- id: file:///cwl/predictions.cwl#extract-tissue-high/batch
source: file:///cwl/predictions.cwl#tissue-high-batch
- id: file:///cwl/predictions.cwl#extract-tissue-high/chunk
source: file:///cwl/predictions.cwl#tissue-high-chunk
- id: file:///cwl/predictions.cwl#extract-tissue-high/filter
source: file:///cwl/predictions.cwl#tissue-high-filter
- id: file:///cwl/predictions.cwl#extract-tissue-high/filter_slide
source: file:///cwl/predictions.cwl#extract-tissue-low/tissue
- id: file:///cwl/predictions.cwl#extract-tissue-high/gpu
source: file:///cwl/predictions.cwl#gpu
- id: file:///cwl/predictions.cwl#extract-tissue-high/label
source: file:///cwl/predictions.cwl#tissue-high-label
- id: file:///cwl/predictions.cwl#extract-tissue-high/level
source: file:///cwl/predictions.cwl#tissue-high-level
- id: file:///cwl/predictions.cwl#extract-tissue-high/mode
source: file:///cwl/predictions.cwl#mode
- id: file:///cwl/predictions.cwl#extract-tissue-high/src
source: file:///cwl/predictions.cwl#unzip/mrxs
out:
- file:///cwl/predictions.cwl#extract-tissue-high/tissue
run:
arguments:
- -o
- $(runtime.outdir)
- --writer
- zip
class: CommandLineTool
cwlVersion: v1.1
id: _:94c10448-c2f4-47e1-83ad-0cbd2254349f
inputs:
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/batch
inputBinding:
prefix: --batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/chunk
inputBinding:
prefix: --chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/filter
inputBinding:
prefix: -F
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/filter_slide
inputBinding:
prefix: --filter-slide
type:
- 'null'
- File
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/gpu
inputBinding:
prefix: --gpu
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/label
inputBinding:
prefix: -f
type: string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/level
inputBinding:
prefix: -l
type: int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/mode
inputBinding:
prefix: --mode
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/src
inputBinding:
position: 1
secondaryFiles:
- pattern: "${\n if (self.nameext == '.mrxs') {\n return {\n class: \"\
File\",\n location: self.location.match(/.*\\//)[0] + \"/\" + self.nameroot,\n\
\ basename: self.nameroot};\n }\n else return null;\n}"
required: false
type: File
outputs:
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/tissue
outputBinding:
glob: $(inputs.src.basename).zip
outputEval: ${self[0].basename=inputs.label + '.zip'; return self;}
type: File
requirements:
- class: DockerRequirement
dockerPull: slaid:0.60.4-develop-tissue_model-extract_tissue_eddl_1.1
- class: InitialWorkDirRequirement
listing:
- $(inputs.src)
- class: InlineJavascriptRequirement
- id: file:///cwl/predictions.cwl#extract-tissue-low
in:
- id: file:///cwl/predictions.cwl#extract-tissue-low/batch
source: file:///cwl/predictions.cwl#tissue-low-batch
- id: file:///cwl/predictions.cwl#extract-tissue-low/chunk
source: file:///cwl/predictions.cwl#tissue-low-chunk
- id: file:///cwl/predictions.cwl#extract-tissue-low/gpu
source: file:///cwl/predictions.cwl#gpu
- id: file:///cwl/predictions.cwl#extract-tissue-low/label
source: file:///cwl/predictions.cwl#tissue-low-label
- id: file:///cwl/predictions.cwl#extract-tissue-low/level
source: file:///cwl/predictions.cwl#tissue-low-level
- id: file:///cwl/predictions.cwl#extract-tissue-low/mode
source: file:///cwl/predictions.cwl#mode
- id: file:///cwl/predictions.cwl#extract-tissue-low/src
source: file:///cwl/predictions.cwl#unzip/mrxs
out:
- file:///cwl/predictions.cwl#extract-tissue-low/tissue
run:
arguments:
- -o
- $(runtime.outdir)
- --writer
- zip
class: CommandLineTool
cwlVersion: v1.1
id: _:94c10448-c2f4-47e1-83ad-0cbd2254349f
inputs:
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/batch
inputBinding:
prefix: --batch
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/chunk
inputBinding:
prefix: --chunk
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/filter
inputBinding:
prefix: -F
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/filter_slide
inputBinding:
prefix: --filter-slide
type:
- 'null'
- File
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/gpu
inputBinding:
prefix: --gpu
type:
- 'null'
- int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/label
inputBinding:
prefix: -f
type: string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/level
inputBinding:
prefix: -l
type: int
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/mode
inputBinding:
prefix: --mode
type:
- 'null'
- string
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/src
inputBinding:
position: 1
secondaryFiles:
- pattern: "${\n if (self.nameext == '.mrxs') {\n return {\n class: \"\
File\",\n location: self.location.match(/.*\\//)[0] + \"/\" + self.nameroot,\n\
\ basename: self.nameroot};\n }\n else return null;\n}"
required: false
type: File
outputs:
- id: file:///cwl/predictions.cwl#extract-tissue-high/run/tissue
outputBinding:
glob: $(inputs.src.basename).zip
outputEval: ${self[0].basename=inputs.label + '.zip'; return self;}
type: File
requirements:
- class: DockerRequirement
dockerPull: slaid:0.60.4-develop-tissue_model-extract_tissue_eddl_1.1
- class: InitialWorkDirRequirement
listing:
- $(inputs.src)
- class: InlineJavascriptRequirement
- id: file:///cwl/predictions.cwl#unzip
in:
- id: file:///cwl/predictions.cwl#unzip/src
source: file:///cwl/predictions.cwl#slide
out:
- file:///cwl/predictions.cwl#unzip/mrxs
run:
baseCommand: unzip-slide
class: CommandLineTool
id: _:071ede3f-8647-42f4-820e-b69610aebd87
inputs:
- id: file:///cwl/predictions.cwl#unzip/run/src
inputBinding:
position: 1
type: File
outputs:
- id: file:///cwl/predictions.cwl#unzip/run/mrxs
outputBinding:
glob: $(inputs.src.nameroot).*
secondaryFiles:
- pattern: "${\n if (self.nameext == '.mrxs') {\n return {\n class: \"\
Directory\",\n path: self.nameroot};\n }\n else return null;\n}"
required: false
type: File
requirements:
- class: InitialWorkDirRequirement
listing:
- $(inputs.src)
- class: InlineJavascriptRequirement
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