parse_tree and clock_model work for test

ktmeaton · Mar 4, 2021 · 3650614 · 3650614
1 parent ffcdab9
commit 3650614
Show file tree

Hide file tree

Showing 6 changed files with 1,896 additions and 141 deletions.
diff --git a/.gitignore b/.gitignore
@@ -31,6 +31,8 @@ results/report/*
 results/snippy_multi/*
 results/snippy_pairwise/*
 results/qualimap/*
+results/parse_tree/*
+results/clock/*
 
 # Project
 project/*/iqtree/*/*ckp.gz

diff --git a/config/snakemake.yaml b/config/snakemake.yaml
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -102,8 +102,10 @@ rule all:
         metadata_all_input,
         # Multiqc
         multiqc_all_input,
-        # IQTREE
+        # Phylo
         iqtree_scf_all_input,
+        # Post-Phylo
+        clock_model_all_input,
         # Plot
         plot_missing_data_all_input,
         # Stats

diff --git a/workflow/notebooks/clock_model.py.ipynb b/workflow/notebooks/clock_model.py.ipynb
@@ -82,9 +82,8 @@
     "SCRIPT_NAME = \"clock\"\n",
     "PREV_SCRIPT_NAME = \"parse_tree\"\n",
     "\n",
-    "#WILDCARDS = snakemake.wildcards\n",
-    "# TESTING\n",
-    "WILDCARDS = [\"all\", \"chromosome\", \"5\"]\n",
+    "WILDCARDS = snakemake.wildcards\n",
+    "# TESTING WILDCARDS = [\"all\", \"chromosome\", \"5\"]\n",
     "READS_ORIGIN = WILDCARDS[0]\n",
     "LOCUS_NAME = WILDCARDS[1]\n",
     "MISSING_DATA = WILDCARDS[2]\n",
@@ -108,8 +107,7 @@
    "outputs": [],
    "source": [
     "project_dir = os.getcwd()\n",
-    "# TESTING\n",
-    "project_dir = os.path.dirname(os.path.dirname(project_dir))\n",
+    "# TESTING project_dir = os.path.dirname(os.path.dirname(project_dir))\n",
     "config_dir = os.path.join(project_dir, \"config\")\n",
     "results_dir = os.path.join(project_dir, \"results\")\n",
     "\n",