Simplify (#27)

* 🎨 Use script Signed-off-by: zethson <[email protected]> * ✨ Simplify language Signed-off-by: zethson <[email protected]> * 🎨 Refactor Signed-off-by: zethson <[email protected]> * 🎨 Wording Signed-off-by: zethson <[email protected]> * 🎨 Simplify Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
laminlabs · Apr 22, 2024 · 82dcc53 · 82dcc53
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diff --git a/docs/mcmicro_02.ipynb b/docs/mcmicro_02.ipynb
@@ -97,7 +97,7 @@
    "id": "e16d2a67",
    "metadata": {},
    "source": [
-    "Now we register our Nextflow run by specifying the pipeline name, its version and its associated reference."
+    "Now we register our Nextflow run by running our [registration script](https://github.com/laminlabs/nextflow-lamin-usecases/blob/main/docs/register_mcmicro_run.py)."
    ]
   },
   {
@@ -107,57 +107,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!python register_nf_run.py -p mcmicro -v 1.0.0 -r https://github.com/labsyspharm/mcmicro"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "863bbe66",
-   "metadata": {},
-   "source": [
-    ":::{dropdown} How to amend a `register_nf_run.py` to register input & output files in LaminDB?\n",
-    "\n",
-    "First we created a Transform for the run:\n",
-    "\n",
-    "```python\n",
-    "parser = argparse.ArgumentParser()\n",
-    "parser.add_argument(\"-p\", \"--pipeline-name\", required=True)\n",
-    "parser.add_argument(\"-v\", \"--pipeline-version\", required=True)\n",
-    "parser.add_argument(\"-r\", \"--pipeline-reference\", required=True)\n",
-    "args = parser.parse_args()\n",
-    "\n",
-    "transform = ln.Transform(\n",
-    "    name=args.pipeline_name,\n",
-    "    version=args.pipeline_version,\n",
-    "    type=\"pipeline\",\n",
-    "    reference=args.pipeline_reference,\n",
-    ")\n",
-    "ln.track(transform=transform)\n",
-    "run = ln.dev.run_context.run\n",
-    "```\n",
-    "\n",
-    "To query input files via LaminDB, we added the following lines:\n",
-    "\n",
-    "```python\n",
-    "mcmicro_input = ln.Artifact.filter(key__startswith=\"exemplar-001\")\n",
-    "input_paths = [input_fastq.stage() for input_fastq in mcmicro_input]\n",
-    "```\n",
-    "\n",
-    "To register the output file and nextflow ID with LaminDB, we added the following line to the last task:\n",
-    "\n",
-    "```python\n",
-    "output = ln.Artifact(\n",
-    "    \"exemplar-001/registration/exemplar-001.ome.tif\", description=\"mcmicro\"\n",
-    ")\n",
-    "output.save()\n",
-    "\n",
-    "nextflow_id = getoutput(f\"nextflow log | awk '/{run.id}/{{print $8}}'\")\n",
-    "run.reference = nextflow_id\n",
-    "run.reference_type = \"nextflow_id\"\n",
-    "run.save()\n",
-    "```\n",
-    "\n",
-    ":::\n"
+    "!python register_mcmicro_run.py"
    ]
   },
   {

diff --git a/docs/register_mcmicro_run.py b/docs/register_mcmicro_run.py
@@ -0,0 +1,25 @@
+from subprocess import getoutput
+
+import lamindb as ln
+
+transform = ln.Transform(
+    name="mcmicro",
+    version="1.0.0",
+    type="pipeline",
+    reference="https://github.com/labsyspharm/mcmicro",
+)
+ln.track(transform=transform)
+run = ln.dev.run_context.run
+
+mcmicro_input = ln.Artifact.filter(key__startswith="exemplar-001")
+input_paths = [input_fastq.stage() for input_fastq in mcmicro_input]
+
+output = ln.Artifact(
+    "exemplar-001/registration/exemplar-001.ome.tif", description="mcmicro"
+)
+output.save()
+
+nextflow_id = getoutput(f"nextflow log | awk '/{run.id}/{{print $8}}'")
+run.reference = nextflow_id
+run.reference_type = "nextflow_id"
+run.save()