add prune target for mugration

ktmeaton · Apr 29, 2021 · 9dc376a · 9dc376a
1 parent ca46113
commit 9dc376a
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Showing 3 changed files with 14 additions and 6 deletions.
diff --git a/autologs b/autologs
diff --git a/workflow/notebooks/plot_phylo.py.ipynb b/workflow/notebooks/plot_phylo.py.ipynb
@@ -82,6 +82,7 @@
    "outputs": [],
    "source": [
     "MISSING_DATA=5\n",
+    "PRUNE=\"full\"\n",
     "JSON_INDENT=2\n",
     "AUSPICE_PREFIX=\"plague-phylogeography-projects_main\""
    ]
@@ -98,10 +99,10 @@
     "auspice_remote_dir = \"/mnt/c/Users/ktmea/Projects/plague-phylogeography-projects/auspice/\"\n",
     "\n",
     "\n",
-    "iqtree_dir    = os.path.join(project_dir, \"iqtree/all/chromosome/full/filter{}/\".format(MISSING_DATA))\n",
-    "lsd_dir       = os.path.join(project_dir, \"lsd/all/chromosome/full/filter{}/\".format(MISSING_DATA))\n",
-    "mugration_dir = os.path.join(project_dir, \"mugration/all/chromosome/full/filter{}/\".format(MISSING_DATA))\n",
-    "snippy_dir    = os.path.join(project_dir, \"snippy_multi/all/chromosome/full/filter{}/\".format(MISSING_DATA))\n",
+    "iqtree_dir    = os.path.join(project_dir, \"iqtree/all/chromosome/{}/filter{}/\".format(PRUNE, MISSING_DATA))\n",
+    "lsd_dir       = os.path.join(project_dir, \"lsd/all/chromosome/{}/filter{}/\".format(PRUNE, MISSING_DATA))\n",
+    "mugration_dir = os.path.join(project_dir, \"mugration/all/chromosome/{}/filter{}/\".format(PRUNE, MISSING_DATA))\n",
+    "snippy_dir    = os.path.join(project_dir, \"snippy_multi/all/chromosome/{}/filter{}/\".format(PRUNE, MISSING_DATA))\n",
     "\n",
     "# ------------------------------------------\n",
     "# Trees\n",
@@ -135,7 +136,7 @@
     "\n",
     "# ------------------------------------------\n",
     "# Output\n",
-    "out_dir = project_dir + \"figures/\"\n",
+    "out_dir = iqtree_dir    = os.path.join(project_dir, \"auspice/all/chromosome/{}/filter{}/\".format(PRUNE, MISSING_DATA))\"\n",
     "if not os.path.exists(out_dir):\n",
     "    os.mkdir(out_dir)"
    ]

diff --git a/workflow/rules/targets.smk b/workflow/rules/targets.smk
@@ -344,6 +344,13 @@ rule mugration_all:
     input:
         mugration_all_input
 
+mugration_prune_all_input = expand(results_dir + "/mugration/all/{locus_name}/prune/filter{missing_data}/metadata.tsv",
+                               locus_name=config["reference_locus_name"],
+                               missing_data = config["snippy_missing_data"])
+rule mugration_prune_all:
+    input:
+        mugration_prune_all_input
+
 #------------------------------------------------------------------------------#
 # Plot
 #------------------------------------------------------------------------------#
+1 −1		README.md
+8 −7		autologs
+4 −0		docs/notes/Notes_Development.md