diff --git a/workflows/bbbc.wic b/workflows/bbbc.wic index c27faad..7f650d9 100644 --- a/workflows/bbbc.wic +++ b/workflows/bbbc.wic @@ -1,17 +1,17 @@ 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 @@ -19,7 +19,7 @@ steps: 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 @@ -27,7 +27,7 @@ steps: outDir: !ii omeconverter.outDir out: - outDir: !& omeconverter.outDir -- montage: + montage: in: filePattern: !ii x00_y03_p{p:dd}_c0.ome.tif inpDir: !* omeconverter.outDir @@ -35,14 +35,14 @@ steps: 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