💄 Prettier dat lineage plot

laminlabs · Aug 17, 2023 · 5bbc2c6 · 5bbc2c6
1 parent 5310ba2
commit 5bbc2c6
Showing 1 changed file with 11 additions and 8 deletions.
diff --git a/docs/guide/bulk_rna_seq.ipynb b/docs/guide/bulk_rna_seq.ipynb
@@ -215,7 +215,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "2219c55e",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "!nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name {ln.dev.run_context.run.id} -resume"
@@ -242,14 +246,13 @@
    "execution_count": null,
    "id": "6e7b5f1d-b00b-43d3-bc46-83b14144a8ba",
    "metadata": {
-    "tags": [
-     "hide-output"
-    ]
+    "tags": []
    },
    "outputs": [],
    "source": [
-    "multiqc_results = ln.File.from_dir(\"rna-seq-results/multiqc/\")\n",
-    "ln.save(multiqc_results)"
+    "# this would register 240 files, we don't need them here\n",
+    "# multiqc_results = ln.File.from_dir(\"rna-seq-results/multiqc/\")\n",
+    "# ln.save(multiqc_results)"
    ]
   },
   {
@@ -259,8 +262,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "multiqc_file = ln.File.filter(key__icontains=\"multiqc_report.html\").one()\n",
-    "multiqc_file"
+    "multiqc_file = ln.File(\"rna-seq-results/multiqc/star_salmon/multiqc_report.html\")\n",
+    "multiqc_file.save()"
    ]
   },
   {