diff --git a/cwl_adapters/image_assembler.cwl b/cwl_adapters/image_assembler.cwl index f6d179f..1b4b1f0 100644 --- a/cwl_adapters/image_assembler.cwl +++ b/cwl_adapters/image_assembler.cwl @@ -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: @@ -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 \ No newline at end of file +# manifest: https://raw.githubusercontent.com/NovagenResearch/image-tools/master/transforms/images/image-assembler-tool/plugin.json \ No newline at end of file diff --git a/cwl_adapters/precompute_slide.cwl b/cwl_adapters/precompute_slide.cwl index 2419170..c90ad4d 100644 --- a/cwl_adapters/precompute_slide.cwl +++ b/cwl_adapters/precompute_slide.cwl @@ -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: @@ -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 diff --git a/workflows/bbbc.py b/workflows/bbbc.py index dd7a31e..f33f3c4 100644 --- a/workflows/bbbc.py +++ b/workflows/bbbc.py @@ -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, diff --git a/workflows/bbbc.wic b/workflows/bbbc.wic index 67cde4b..4a032e2 100644 --- a/workflows/bbbc.wic +++ b/workflows/bbbc.wic @@ -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