fix: use virtool-workflow==2.0.0

* Use updated base image and Python package.
* Combine upload steps into single finalize step.
* Add `display_name` and `description` parameters where appropriate.

Author: igboyes

Dockerfile

@@ -1,4 +1,4 @@
-FROM virtool/workflow:1.1.0
+FROM virtool/workflow:2.0.0
 
 WORKDIR /app
 

poetry.lock

@@ -8,7 +8,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.8"
-virtool-workflow = "^1.0.0"
+virtool-workflow = "^2.0.0"
 
 [tool.poetry.dev-dependencies]
 autopep8 = "^1.5.7"

pyproject.toml

@@ -26,22 +26,25 @@ async def run_fastqc(
     intermediate: SimpleNamespace,
     read_files,
 ):
-    """Run `fastqc` on the read files. Parse the output into a dictionary and add it to the scope."""
-    intermediate.quality = await fastqc(read_files)
+    """
+    Run `fastqc` on the read files.
 
-    return "Fastqc run completed."
+    Parse the output into a dictionary and add it to the scope.
+    """
+    intermediate.quality = await fastqc(read_files)
 
 
 @step
-async def upload_read_files(sample_provider: SampleProvider, read_files):
-    """Upload the read files."""
+async def finalize(intermediate: SimpleNamespace, sample_provider: SampleProvider, read_files):
+    """
+    Save the sample data in Virtool.
+
+    * Upload the read files to the sample file endpoints.
+    * POST the JSON quality data to sample endpoint.
+    """
     for file in read_files:
         await sample_provider.upload(file)
 
-
-@step
-async def upload_quality(sample_provider: SampleProvider, intermediate: SimpleNamespace):
-    """Upload the resulting quality to the sample record."""
     await sample_provider.finalize(intermediate.quality)