Update file examples (#1067)

Author: dorien-er

CHANGELOG.md

@@ -46,6 +46,8 @@
 
 * Bump anndata to `0.12.11` (PR #1174).
 
+* Add missing `example` fields to several component and workflow configurations (PR #1067).
+
 * Testing: bump `viashpy` to 0.10.0 (PR #1178).
 
 ## BUG FIXES

src/annotate/onclass/config.vsh.yaml

@@ -51,14 +51,17 @@ argument_groups:
         type: file
         description: The .nlp.emb file with the cell type embeddings.
         required: true
+        example: cl.ontology.nlp.emb
       - name: "--cl_ontology_file"
         type: file
         description: The .ontology file with the cell type ontology.
         required: true
+        example: cl.ontology
       - name: "--cl_obo_file"
         type: file
         description: The .obo file with the cell type ontology.
         required: true
+        example: cl.obo
 
   - name: Reference
     description: Arguments related to the reference dataset.

src/annotate/scanvi/config.vsh.yaml

@@ -21,6 +21,7 @@ argument_groups:
         description: Input h5mu file. Note that this needs to be the exact same dataset as the --scvi_model was trained on.
         direction: input
         required: true
+        example: input.h5mu
       - name: "--modality"
         description: |
           Which modality from the input MuData file to process.
@@ -67,6 +68,7 @@ argument_groups:
       - name: "--output"
         alternatives: ["-o"]
         type: file
+        example: output.h5mu
         description: Output h5mu file.
         direction: output
         required: true
@@ -75,6 +77,7 @@ argument_groups:
         description: Folder where the state of the trained model will be saved to.
         required: false
         direction: output
+        example: path/to/output_model/
       - name: "--obsm_output"
         type: string
         default: "X_scanvi_integrated"

src/compression/compress_h5mu/config.vsh.yaml

@@ -12,13 +12,14 @@ arguments:
     type: file
     description: Path to the input .h5mu.
     required: true
-    example: sample_path
+    example: input.h5mu
     direction: input
   - name: "--output"
     type: file
     description: location of output file.
     required: true
     direction: output
+    example: output.h5mu
 __merge__: [., /src/base/h5_compression_argument.yaml]
 resources:
   - type: python_script

src/convert/from_10xh5_to_h5mu/config.vsh.yaml

@@ -19,7 +19,7 @@ argument_groups:
       - name: "--input_metrics_summary"
         type: file
         description: A metrics summary csv file as generated by Cell Ranger.
-        example: metrics_cellranger.h5
+        example: metrics_cellranger.csv
   - name: Outputs
     arguments:
       - name: "--output"

src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml

@@ -12,14 +12,14 @@ arguments:
     type: file
     must_exist: true
     description: Input SAM or BAM file.
-    example: input.bam
+    example: "input.bam"
     direction: input
     required: true
   - name: "--output"
     alternatives: ["-o"]
     type: file
     description: Output alignment file.
-    example: output.sam
+    example: "output.bam"
     direction: output
   - name: "--bam"
     type: boolean_true

src/convert/from_h5mu_or_h5ad_to_tiledb/config.vsh.yaml

@@ -126,6 +126,7 @@ argument_groups:
     arguments:
       - name: "--tiledb_dir"
         type: file
+        example: path/to/tiledb_dir
         direction: output
         description: |
           Directory where the TileDB output will be written to.

src/dataflow/merge/config.vsh.yml

@@ -14,6 +14,7 @@ arguments:
     description: Paths to the single-modality .h5mu files that need to be combined
     required: true
     default: sample_paths
+    example: ["/path/to/modality_1.h5mu", "/path/to/modality_2.h5mu"]
   - name: "--output"
     description: Path to the output file.
     alternatives: ["-o"]

src/dataflow/split_h5mu/config.vsh.yaml

@@ -13,6 +13,7 @@ argument_groups:
     type: file
     description: Path to a single .h5mu file.
     required: true
+    example: input.h5mu
   - name: "--modality"
     description: |
       Which modality from the input MuData file to process.

src/dataflow/split_modalities/config.vsh.yaml

@@ -15,6 +15,7 @@ arguments:
     description: Path to a single .h5mu file.
     required: true
     default: sample_path
+    example: input.h5mu
   - name: "--output"
     alternatives: ["-o"]
     type: file