bbbc.wic

steps:
  bbbcdownload:
    in:
      name: !ii BBBC001
      outDir: !ii bbbcdownload.outDir
    out:
    - outDir: !& bbbcdownload.outDir
  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:
    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:
    in:
      fileExtension: !ii .ome.tif
      filePattern: !ii .*.tif
      inpDir: !* file-renaming.outDir
      outDir: !ii omeconverter.outDir
    out:
    - outDir: !& omeconverter.outDir
  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:
    in:
      imgPath: !* omeconverter.outDir
      outDir: !ii image_assembler.outDir
      stitchPath: !* montage.outDir
    out:
    - outDir: !& image_assembler.outDir
  precompute_slide:
    in:
      imageType: !ii image
      inpDir: !* image_assembler.outDir
      outDir: !ii precompute_slide.outDir
      pyramidType: !ii Zarr