Merge pull request #17 from jfennick/wic_inline_input

add !ii inline input custom yaml tag

Author: sameeul

.vscode/settings.json

@@ -2,6 +2,8 @@
     "yaml.customTags": [
         "!&",
         "!*",
-        "!ii"
+        "!ii",
+        "!ii mapping",
+        "!ii sequence"
     ]
 }

workflows/bbbc.yml

@@ -1,50 +1,50 @@
 steps:
 - bbbcdownload:
     in:
-      name: BBBC001
-      outDir: bbbcdownload.outDir
+      name: !ii BBBC001
+      outDir: !ii bbbcdownload.outDir
     out:
     - outDir: !& bbbcdownload.outDir
 - subdirectory:
     in:
       directory: !* bbbcdownload.outDir
-      glob_pattern: bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
+      glob_pattern: !ii bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
     out:
     - subdirectory: !& subdirectory.subdirectory
 - file-renaming:
     in:
-      filePattern: .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
+      filePattern: !ii .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
       inpDir: !* subdirectory.subdirectory
-      outDir: file-renaming.outDir
-      outFilePattern: x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif
+      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: .ome.tif
-      filePattern: .*.tif
+      fileExtension: !ii .ome.tif
+      filePattern: !ii .*.tif
       inpDir: !* file-renaming.outDir
-      outDir: omeconverter.outDir
+      outDir: !ii omeconverter.outDir
     out:
     - outDir: !& omeconverter.outDir
 - montage:
     in:
-      filePattern: x00_y03_p{p:dd}_c0.ome.tif
+      filePattern: !ii x00_y03_p{p:dd}_c0.ome.tif
       inpDir: !* omeconverter.outDir
-      layout: p
-      outDir: montage.outDir
+      layout: !ii p
+      outDir: !ii montage.outDir
     out:
     - outDir: !& montage.outDir
 - image_assembler:
     in:
       imgPath: !* omeconverter.outDir
-      outDir: image_assembler.outDir
+      outDir: !ii image_assembler.outDir
       stitchPath: !* montage.outDir
     out:
     - outDir: !& image_assembler.outDir
 - precompute_slide:
     in:
-      imageType: image
+      imageType: !ii image
       inpDir: !* image_assembler.outDir
-      outDir: precompute_slide.outDir
-      pyramidType: Zarr
+      outDir: !ii precompute_slide.outDir
+      pyramidType: !ii Zarr