Merge pull request #16 from jfennick/custom_tag_explicit_edge_syntax

Custom tag explicit edge syntax

Author: sameeul

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "yaml.customTags": [
+        "!&",
+        "!*",
+        "!ii"
+    ]
+}

workflows/bbbc.py

@@ -11,7 +11,6 @@ def workflow() -> Workflow:
     subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
     subdirectory.directory = bbbcdownload.outDir
     subdirectory.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
-    subdirectory.subdirectory = Path('subdirectory.subdirectory')
 
     filerenaming = Step(clt_path='../image-workflows/cwl_adapters/file-renaming.cwl')
     # NOTE: FilePattern {} syntax shadows python f-string {} syntax

workflows/bbbc.yml

@@ -2,38 +2,49 @@ steps:
 - bbbcdownload:
     in:
       name: BBBC001
-      outDir: '&bbbcdownload.outDir'
+      outDir: bbbcdownload.outDir
+    out:
+    - outDir: !& bbbcdownload.outDir
 - subdirectory:
     in:
-      directory: '*bbbcdownload.outDir'
+      directory: !* bbbcdownload.outDir
       glob_pattern: bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/
-      subdirectory: '&subdirectory.subdirectory'
+    out:
+    - subdirectory: !& subdirectory.subdirectory
 - file-renaming:
     in:
       filePattern: .*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif
-      inpDir: '*subdirectory.subdirectory'
-      outDir: '&file-renaming.outDir'
+      inpDir: !* subdirectory.subdirectory
+      outDir: file-renaming.outDir
       outFilePattern: 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
-      inpDir: '*file-renaming.outDir'
-      outDir: '&omeconverter.outDir'
+      inpDir: !* file-renaming.outDir
+      outDir: omeconverter.outDir
+    out:
+    - outDir: !& omeconverter.outDir
 - montage:
     in:
       filePattern: x00_y03_p{p:dd}_c0.ome.tif
-      inpDir: '*omeconverter.outDir'
+      inpDir: !* omeconverter.outDir
       layout: p
-      outDir: '&montage.outDir'
+      outDir: montage.outDir
+    out:
+    - outDir: !& montage.outDir
 - image_assembler:
     in:
-      imgPath: '*omeconverter.outDir'
-      outDir: '&image_assembler.outDir'
-      stitchPath: '*montage.outDir'
+      imgPath: !* omeconverter.outDir
+      outDir: image_assembler.outDir
+      stitchPath: !* montage.outDir
+    out:
+    - outDir: !& image_assembler.outDir
 - precompute_slide:
     in:
       imageType: image
-      inpDir: '*image_assembler.outDir'
+      inpDir: !* image_assembler.outDir
       outDir: precompute_slide.outDir
       pyramidType: Zarr

workflows/bbbc_sub.py

@@ -13,7 +13,6 @@ def workflow() -> Workflow:
     subdirectory = Step(clt_path='../workflow-inference-compiler/cwl_adapters/subdirectory.cwl')
     subdirectory.directory = bbbcdownload.outDir
     subdirectory.glob_pattern = 'bbbcdownload.outDir/BBBC/BBBC001/raw/Images/human_ht29_colon_cancer_1_images/'
-    subdirectory.subdirectory = Path('subdirectory.subdirectory')
 
     filerenaming = Step(clt_path='cwl_adapters/file-renaming.cwl')
     # NOTE: FilePattern {} syntax shadows python f-string {} syntax
@@ -46,7 +45,6 @@ def workflow2() -> Workflow:
     # i.e. This is the API for the subworkflow.
     subworkflow.steps[0].directory = subworkflow.directory
     subworkflow.steps[0].glob_pattern = subworkflow.glob_pattern
-    subworkflow.steps[0].subdirectory = Path('subdirectory.subdirectory')
 
     # Then apply arguments at the call site.
     # Notice how the caller does not need to know about the internal details of the subworkflow