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Merge pull request #2 from ResearchObject/dh_pipeline_example
Add DeepHealth tissue/tumor prediction pipeline example
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| ro-crate-preview.html |
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docs/examples/draft/ml-predict-pipeline/predictions.cwl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,382 @@ | ||
| 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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