update subset cosmx scope to private

CHANGELOG.md

@@ -1,3 +1,9 @@
+# openpipeline_spatial x.x.x
+
+## MINOR CHANGES
+
+* Add `scope` to component and workflow configurations (PR #22).
+
 # openpipeline_spatial 0.1.1
 
 ## MINOR CHANGES

src/convert/from_cosmx_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_cosmx_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Converts the output from NanoString experiment into a MuData objcet.
     - `<dataset_id>_exprMat_file.csv`: File containing the counts.

src/convert/from_spatialdata_to_h5mu/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_spatialdata_to_h5mu"
 namespace: "convert"
+scope: "public"
 description: |
   Reads in the Tables field stored in a SpatialData object and converts it to an h5mu file.
 

src/convert/from_xenium_to_spatialdata/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: "from_xenium_to_spatialdata"
 namespace: "convert"
+scope: "public"
 description: |
   Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet.
   By default, the following files will be converted:

src/filter/subset_cosmx/config.vsh.yaml

@@ -1,4 +1,5 @@
 name: "subset_cosmx"
+scope: "private"
 namespace: "filter"
 description: |
   Filters the output from NanoString experiment to keep only a subset of the fields of view.

src/mapping/spaceranger_count/config.vsh.yaml

@@ -1,5 +1,6 @@
 name: spaceranger_count
 namespace: mapping
+scope: public
 description: Count gene expression and protein expression reads from a single capture area.
 keywords: [spaceranger]
 links: