add auspice to snakemake

ktmeaton · Apr 29, 2021 · a103420 · a103420
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diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -1,3 +1,4 @@
 # Development
 
 1. Add mugration to workflow.
+1. Upgrade auspice to 2.25.1
diff --git a/results/config/auspice_config.json b/results/config/auspice_config.json
@@ -1,36 +1,26 @@
 {
   "title": "Plague Phylogeography Test",
-  "build_url": "https://github.com/ktmeaton/plague-phylogeography-projects/tree/tree",
+  "build_url": "https://github.com/ktmeaton/plague-phylogeography-projects/tree/test",
   "maintainers": [
     {
       "name": "Katherine Eaton",
       "url": "https://ktmeaton.github.io"
     }
   ],
   "colorings": [
-    {
-      "key": "scf",
-      "title": "sCF",
-      "type": "continuous"
-    },
     {
       "key": "biosample_accession",
       "title": "BioSample Accession",
       "type": "categorical"
     },
     {
-      "key": "biosample_comment",
-      "title": "BioSample Comment",
+      "key": "branch_major",
+      "title": "Branch Major",
       "type": "categorical"
     },
     {
-      "key": "biovar",
-      "title": "Biovar",
-      "type": "categorical"
-    },
-    {
-      "key": "branch_major",
-      "title": "Branch Major",
+      "key": "branch_major_conf_category",
+      "title": "Branch Major Confidence",
       "type": "categorical"
     },
     {
@@ -39,120 +29,84 @@
       "type": "categorical"
     },
     {
-      "key": "branch_number",
-      "title": "Branch Number",
+      "key": "branch_minor_conf_category",
+      "title": "Branch Minor Confidence",
       "type": "categorical"
     },
     {
-      "key": "continent",
-      "title": "Continent",
+      "key": "branch_number",
+      "title": "Branch Number",
       "type": "categorical"
     },
     {
-      "key": "country",
-      "title": "Country",
-      "type": "categorical"
+      "key": "branch_support",
+      "title": "Branch Support",
+      "type": "continuous"
     },
     {
-      "key": "date_bp",
-      "title": "Collection Date (BP)",
+      "key": "clade_rtt_dist",
+      "title": "Clade Root Distance",
       "type": "continuous"
     },
     {
-      "key": "node_type",
-      "title": "Node Type",
+      "key": "continent",
+      "title": "Continent",
       "type": "categorical"
     },
     {
-      "key": "province",
-      "title": "Province",
+      "key": "country",
+      "title": "Country",
       "type": "categorical"
     },
     {
-      "key": "rate",
-      "title": "Substitution Rate",
-      "type": "continuous"
-    },
-    {
-      "key": "rate_fold_change",
-      "title": "Substitution Rate Fold Change",
-      "type": "continuous"
-    },
-    {
-      "key": "raw_date",
-      "title": "Collection Date",
-      "type": "continuous"
-    },
-    {
-      "key": "strain",
-      "title": "Strain",
+      "key": "country_conf_category",
+      "title": "Country Confidence",
       "type": "categorical"
     },
     {
-      "key": "ufboot",
-      "title": "Ultrafast Bootstrap",
-      "type": "continuous"
-    },
-    {
-    "key": "chrom_cov",
-    "title": "Chromosome Coverage",
-    "type": "continuous"
-    },
-    {
-      "key": "pcd1_cov",
-      "title": "pCD1 Coverage",
-      "type": "continuous"
-    },
-    {
-      "key": "pmt1_cov",
-      "title": "pMT1 Coverage",
+      "key": "date_bp_mean",
+      "title": "Collection Date (BP)",
       "type": "continuous"
     },
     {
-      "key": "ppcp1_cov",
-      "title": "pPCP1 Coverage",
+      "key": "date_mean",
+      "title": "Collection Date",
       "type": "continuous"
     },
     {
-      "key": "pla_cov",
-      "title": "pla Coverage",
+      "key": "date_err",
+      "title": "Collection Date Uncertainty",
       "type": "continuous"
     },
     {
-    "key": "chrom_dep",
-    "title": "Chromosome Depth",
-    "type": "continuous"
-    },
-    {
-      "key": "pcd1_dep",
-      "title": "pCD1 Depth",
-      "type": "continuous"
+      "key": "node_type",
+      "title": "Node Type",
+      "type": "categorical"
     },
     {
-      "key": "pmt1_dep",
-      "title": "pMT1 Depth",
-      "type": "continuous"
+      "key": "province",
+      "title": "Province",
+      "type": "categorical"
     },
     {
-      "key": "ppcp1_dep",
-      "title": "pPCP1 Depth",
-      "type": "continuous"
+      "key": "province_conf_category",
+      "title": "Province Confidence",
+      "type": "categorical"
     },
     {
-      "key": "pla_dep",
-      "title": "pla Depth",
+      "key": "root_rtt_dist",
+      "title": "Root Distance",
       "type": "continuous"
     },
     {
-      "key": "ppcp1_pla_dep_ratio",
-      "title": "pPCP1 pla Depth Ratio",
-      "type": "continuous"
+      "key": "strain",
+      "title": "Strain",
+      "type": "categorical"
     }
   ],
   "filters": [
     "country",
     "province",
-    "biovar",
     "branch_major",
     "branch_minor"
   ],
@@ -167,9 +121,11 @@
   ],
   "display_defaults": {
     "color_by": "branch_major",
-    "distance_measure": "div",
+    "distance_measure": "num_date",
     "geo_resolution": "province",
     "map_triplicate": true,
-    "branch_label": "none"
+    "branch_label": "none",
+    "transmission_lines": true,
+    "layout": "rect"
   }
 }
diff --git a/results/config/snakemake.yaml b/results/config/snakemake.yaml
@@ -97,10 +97,10 @@ snippy_multi_plot_missing_data:
 iqtree_model : "-m K3Pu+F+I"
 iqtree_seed : "47321424" # keeping it consistent in a config file allows for checkpointing
 iqtree_runs : 1
-iqtree_other : "--ufboot 1000"
+iqtree_other : ""
 
 # Outgroup Option #1: Reference
-iqtree_outgroup : "Reference"
+#iqtree_outgroup : "Reference"
 
 # Outgroup Option #2: Basal modern clade
 #iqtree_outgroup : "GCA_000323485.1_ASM32348v1_genomic,GCA_000323845.1_ASM32384v1_genomic"
@@ -109,4 +109,10 @@ iqtree_outgroup : "Reference"
 #iqtree_outgroup : "SAMEA3541826"
 
 # Outgroup Option #4: Outgroup
-#iqtree_outgroup : "GCA_900637475.1_51108_B01_genomic,GCA_000834295.1_ASM83429v1_genomic"
+iqtree_outgroup : "GCA_900637475.1_51108_B01_genomic,GCA_000834295.1_ASM83429v1_genomic"
+
+mugration_attribute:
+  - branch_major
+  - branch_minor
+  - country
+  - province
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -117,9 +117,11 @@ rule all:
         snippy_multi_filter_prune_all_input,
         # Phylo
         #iqtree_all_input,
-        iqtree_filter_all_input,
+        #iqtree_filter_all_input,
         # Post-Phylo (no lsd2 for gh actions)
         #lsd_all_input,
+        mugration_all_input,
+        mugration_prune_all_input,
         # Plot
         plot_missing_data_all_input,
         plot_snp_matrix_all_input,

diff --git a/workflow/envs/main/environment.yaml b/workflow/envs/main/environment.yaml
@@ -67,3 +67,5 @@ dependencies:
     #- phylo-treetime==0.8.1
     - nextstrain-augur==10.3.0
     - bezier==2020.5.19
+# npm:
+# - auspice@2.23.0 -> @2.25.1
diff --git a/workflow/envs/merge/environment.yaml b/workflow/envs/merge/environment.yaml
@@ -95,3 +95,5 @@ dependencies:
   - nextstrain-augur==10.3.0
   - bezier==2020.5.19
 name: plague-phylogeography
+# npm:
+# - auspice@2.23.0 -> @2.25.1