pass min-seq-len as parameter to report notebook

Author: alpae

FastOMA.nf

@@ -413,6 +413,7 @@ process fastoma_report {
     papermill $notebook \
               report.ipynb \
               -p output_folder "./" \
+              -p min_sequence_length ${params.min_sequence_length} \
               -p proteome_folder "$proteome_folder"
 
     jupyter nbconvert --to html report.ipynb

FastOMA/fastoma_notebook_stat.ipynb

@@ -87,12 +87,13 @@
      "parameters"
     ]
    },
+   "outputs": [],
    "source": [
     "output_folder = \"Output\"\n",
     "input_folder = \"testdata/in_folder\"\n",
-    "proteome_folder = input_folder + \"/proteome\""
-   ],
-   "outputs": []
+    "proteome_folder = input_folder + \"/proteome\"\n",
+    "min_sequence_length = 50"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -129,9 +130,10 @@
     },
     "tags": []
    },
+   "outputs": [],
    "source": [
     "def get_protein_dataframe(folder):\n",
-    "    species, seq_reqs, _ = parse_proteomes(folder,min_sequence_length=50) \n",
+    "    species, seq_reqs, _ = parse_proteomes(folder,min_sequence_length=min_sequence_length) \n",
     "    print(f\"There are {len(species)} species in the proteome folder.\")\n",
     "    print(f\"In total, {sum(len(z) for z in seq_reqs.values())} proteins are in the dataset.\")\n",
     "    print(\"\\nThe list of species is the following:\")\n",