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workflows/bbbc.wic

+7-7
Original file line numberDiff line numberDiff line change
@@ -1,48 +1,48 @@
11
steps:
2-
- bbbcdownload:
2+
bbbcdownload:
33
in:
44
name: !ii BBBC001
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outDir: !ii bbbcdownload.outDir
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out:
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- outDir: !& bbbcdownload.outDir
8-
- subdirectory:
8+
subdirectory:
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in:
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directory: !* bbbcdownload.outDir
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glob_pattern: !ii bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
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out:
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- subdirectory: !& subdirectory.subdirectory
14-
- file-renaming:
14+
file-renaming:
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in:
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filePattern: !ii .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
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inpDir: !* subdirectory.subdirectory
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outDir: !ii file-renaming.outDir
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outFilePattern: !ii x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif
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out:
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- outDir: !& file-renaming.outDir
22-
- ome-converter:
22+
ome-converter:
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in:
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fileExtension: !ii .ome.tif
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filePattern: !ii .*.tif
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inpDir: !* file-renaming.outDir
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outDir: !ii omeconverter.outDir
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out:
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- outDir: !& omeconverter.outDir
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- montage:
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montage:
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in:
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filePattern: !ii x00_y03_p{p:dd}_c0.ome.tif
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inpDir: !* omeconverter.outDir
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layout: !ii p
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outDir: !ii montage.outDir
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out:
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- outDir: !& montage.outDir
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- image_assembler:
38+
image_assembler:
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in:
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imgPath: !* omeconverter.outDir
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outDir: !ii image_assembler.outDir
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stitchPath: !* montage.outDir
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out:
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- outDir: !& image_assembler.outDir
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- precompute_slide:
45+
precompute_slide:
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in:
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imageType: !ii image
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inpDir: !* image_assembler.outDir

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