update deps for notebook building

dib-lab · Nov 6, 2020 · 2d5d509 · 2d5d509
1 parent 712e55b
commit 2d5d509
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/genome_grist/conf/Snakefile b/genome_grist/conf/Snakefile
@@ -298,6 +298,7 @@ rule make_notebook:
 
 rule make_html:
     input:
+        source_nb='genome_grist/notebooks/report-sample.ipynb',
         notebook = outdir + f'/reports/report-{SAMPLE}.ipynb'
     output:
         outdir + f'/reports/report-{SAMPLE}.html'

diff --git a/genome_grist/notebooks/report-sample.ipynb b/genome_grist/notebooks/report-sample.ipynb
@@ -26,6 +26,17 @@
     "#sample_id = 'p8808mo11'\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from IPython.display import Markdown as md\n",
+    "from IPython.display import display\n",
+    "md(f\"# genome-grist report for metagenome `{sample_id}`\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -48,7 +59,7 @@
     "gather_df = pd.read_csv(f'../../outputs/{sample_id}.gather.csv')\n",
     "\n",
     "# names!\n",
-    "names_df = pd.read_csv(f'../../{sample_id}.acc.urls.csv')\n",
+    "names_df = pd.read_csv(f'../../outputs/genbank/{sample_id}.genomes.info.csv')\n",
     "\n",
     "# connect gather_df to all_df and left_df using 'genome_id'\n",
     "def fix_name(x):\n",