🎨 Polish

Signed-off-by: zethson <[email protected]>

docs/nf_core_scrnaseq.ipynb

@@ -19,7 +19,7 @@
     "1. Using a serverless environment trigger (e.g., AWS Lambda) to execute a Python script.\n",
     "2. By using a [post-run script](https://docs.seqera.io/platform/23.4.0/launch/advanced#pre-and-post-run-scripts) on the Seqera Platform.\n",
     "\n",
-    "Both approaches execute a script that connects to the Lamindb instance and registers the run output, similar to the one shown below.\n",
+    "Both approaches execute a script that connects to the Lamindb instance and registers the run input, output, and metadata, as shown below.\n",
     "\n",
     "This guide shows how to manually register a Nextflow run and illustrates what such an automated script could look like by registering the output of a run of the [nf-core/scrnaseq](https://nf-co.re/scrnaseq/latest) pipeline into a lamin instance."
    ]
@@ -42,11 +42,14 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "3358a50f",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "import lamindb as ln\n",
-    "import anndata as ad"
+    "import lamindb as ln"
    ]
   },
   {
@@ -233,7 +236,7 @@
    "id": "5f3f95a8",
    "metadata": {
     "tags": [
-     "hidden"
+     "hide-output"
     ]
    },
    "outputs": [],

docs/register_scrnaseq_run.py

@@ -6,14 +6,14 @@
 
 
 def parse_arguments() -> argparse.Namespace:
-    parser = argparse.ArgumentParser(description="Register nf-core/scrnaseq run in LaminDB.")
-    parser.add_argument("--input", type=str, required=True, help="Nextflow run input folder path.")
-    parser.add_argument("--output", type=str, required=True, help="Nextflow run output folder path.")
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--input", type=str, required=True)
+    parser.add_argument("--output", type=str, required=True)
     return parser.parse_args()
 
 
 def register_pipeline_io(input_dir: str, output_dir: str, global_run: ln.Run) -> None:
-    """Registers input and output files and folders of a nf-core/scrnaseq run."""
+    """Registers input and output files and folders for an nf-core/scrnaseq run."""
     input_artifacts = ln.Artifact.from_dir(input_dir, run=False)
     ln.save(input_artifacts)
     global_run.input_artifacts.set(input_artifacts)
@@ -25,7 +25,7 @@ def register_pipeline_io(input_dir: str, output_dir: str, global_run: ln.Run) ->
 
 
 def register_pipeline_metadata(output_dir: str, global_run: ln.Run) -> None:
-    """Registers nf-core pipeline run metadata stored in the 'pipeline_info' directory."""
+    """Registers nf-core pipeline run metadata stored in the 'pipeline_info' folder."""
     ulabel = ln.ULabel(name="nextflow").save()
     global_run.transform.ulabels.add(ulabel)