💄 Prettify guide

docs/guide/bulk_rna_seq.ipynb

@@ -5,7 +5,7 @@
    "id": "a1c40541-e05e-48a3-8b50-33baf3d6d0d4",
    "metadata": {},
    "source": [
-    "# Tracking Bulk RNA-seq Nextflow runs"
+    "# Track bulk RNA-seq Nextflow runs"
    ]
   },
   {
@@ -56,6 +56,23 @@
     "!lamin init --storage ./nextflow_rna_seq --schema bionty"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ca2926f4",
+   "metadata": {
+    "tags": [
+     "hide-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# avoids download bars\n",
+    "import bionty as bt\n",
+    "\n",
+    "bt.Gene(species=\"saccharomyces cerevisiae\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -149,7 +166,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "e80ed3ad-3588-4b47-9720-66fbe7492ffd",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "input_fastqs_file = ln.File.from_dir(\"test-datasets/testdata/GSE110004/\")\n",
@@ -238,7 +259,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "6e7b5f1d-b00b-43d3-bc46-83b14144a8ba",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "multiqc_results = ln.File.from_dir(\"rna-seq-results/multiqc/\", run=run)\n",
@@ -337,6 +362,20 @@
    "source": [
     "Lamin makes it easy to track pipeline executions and to ingest input and output files that can subsequently be used for advanced downstream analyses. This is complementary to nf-tower."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5f3f95a8",
+   "metadata": {
+    "tags": [
+     "hide-cell"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "!lamin delete --force nextflow_rna_seq"
+   ]
   }
  ],
  "metadata": {