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fix: move image_assembler and precompute_slide to the image-tools images #27

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Merged
sameeul merged 1 commit into from
Oct 13, 2026
Merged

fix: move image_assembler and precompute_slide to the image-tools images #27

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6 changes: 3 additions & 3 deletions cwl_adapters/image_assembler.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@ label: Image Assembler

doc: |-
This plugin assembles images into a stitched image using an image stitching vector.
https://github.com/PolusAI/polus-plugins/tree/master/transforms/images/image-assembler-plugin
https://github.com/NovagenResearch/image-tools/tree/master/transforms/images/image-assembler-tool

requirements:
DockerRequirement:
dockerPull: polusai/image-assembler-plugin:1.4.0-dev0
dockerPull: polusai/image-assembler-tool:1.4.3
# See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
InitialWorkDirRequirement:
listing:
Expand Down Expand Up @@ -94,4 +94,4 @@ $namespaces:
$schemas:
- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

# manifest: https://raw.githubusercontent.com/PolusAI/polus-plugins/master/transforms/images/image-assembler-plugin/plugin.json
# manifest: https://raw.githubusercontent.com/NovagenResearch/image-tools/master/transforms/images/image-assembler-tool/plugin.json
8 changes: 4 additions & 4 deletions cwl_adapters/precompute_slide.cwl
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Expand Up @@ -6,11 +6,11 @@ label: Precompute Slide

doc: |-
This plugin generates image pyramids in multiple viewing formats.
https://github.com/PolusAI/polus-plugins/tree/master/visualization/polus-precompute-slide-plugin
https://github.com/NovagenResearch/image-tools/tree/master/visualization/precompute-slide-tool

requirements:
DockerRequirement:
dockerPull: polusai/precompute-slide-plugin:1.7.0-dev0
dockerPull: polusai/precompute-slide-tool:1.7.3-dev0
# See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement
InitialWorkDirRequirement:
listing:
Expand All @@ -36,9 +36,9 @@ inputs:
prefix: --pyramidType

imageType:
label: Image is either Segmentation or Image
label: Image is either Intensity or Segmentation
doc: |-
Image is either Segmentation or Image
Image is either Intensity or Segmentation
inputBinding:
prefix: --imageType
type: string
Expand Down
2 changes: 1 addition & 1 deletion workflows/bbbc.py
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Expand Up @@ -39,7 +39,7 @@ def workflow() -> Workflow:
precompute_slide = Step(clt_path='cwl_adapters/precompute_slide.cwl')
precompute_slide.inpDir = image_assembler.outDir
precompute_slide.pyramidType = 'Zarr'
precompute_slide.imageType = 'image'
precompute_slide.imageType = 'Intensity'
precompute_slide.outDir = Path('precompute_slide.outDir')

steps = [bbbcdownload,
Expand Down
2 changes: 1 addition & 1 deletion workflows/bbbc.wic
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Expand Up @@ -43,7 +43,7 @@ steps:
- outDir: !& image_assembler.outDir
precompute_slide:
in:
imageType: !ii image
imageType: !ii Intensity
inpDir: !* image_assembler.outDir
outDir: !ii precompute_slide.outDir
pyramidType: !ii Zarr
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