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use canonical normal form(s) #19

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May 7, 2024
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14 changes: 7 additions & 7 deletions workflows/bbbc.wic
Original file line number Diff line number Diff line change
@@ -1,48 +1,48 @@
steps:
- bbbcdownload:
bbbcdownload:
in:
name: !ii BBBC001
outDir: !ii bbbcdownload.outDir
out:
- outDir: !& bbbcdownload.outDir
- subdirectory:
subdirectory:
in:
directory: !* bbbcdownload.outDir
glob_pattern: !ii bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
out:
- subdirectory: !& subdirectory.subdirectory
- file-renaming:
file-renaming:
in:
filePattern: !ii .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
inpDir: !* subdirectory.subdirectory
outDir: !ii file-renaming.outDir
outFilePattern: !ii x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif
out:
- outDir: !& file-renaming.outDir
- ome-converter:
ome-converter:
in:
fileExtension: !ii .ome.tif
filePattern: !ii .*.tif
inpDir: !* file-renaming.outDir
outDir: !ii omeconverter.outDir
out:
- outDir: !& omeconverter.outDir
- montage:
montage:
in:
filePattern: !ii x00_y03_p{p:dd}_c0.ome.tif
inpDir: !* omeconverter.outDir
layout: !ii p
outDir: !ii montage.outDir
out:
- outDir: !& montage.outDir
- image_assembler:
image_assembler:
in:
imgPath: !* omeconverter.outDir
outDir: !ii image_assembler.outDir
stitchPath: !* montage.outDir
out:
- outDir: !& image_assembler.outDir
- precompute_slide:
precompute_slide:
in:
imageType: !ii image
inpDir: !* image_assembler.outDir
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