revert default config to test

ktmeaton · Apr 19, 2021 · 28af620 · 28af620
1 parent f8e76ad
commit 28af620
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Showing 2 changed files with 23 additions and 13 deletions.
diff --git a/results/config/auspice_config.json b/results/config/auspice_config.json
@@ -1,6 +1,6 @@
 {
-  "title": "Plague Phylogeography Placement",
-  "build_url": "https://github.com/ktmeaton/plague-phylogeography-projects/tree/main/placement",
+  "title": "Plague Phylogeography Test",
+  "build_url": "https://github.com/ktmeaton/plague-phylogeography-projects/tree/main/test",
   "maintainers": [
     {
       "name": "Katherine Eaton",

diff --git a/results/config/snakemake.yaml b/results/config/snakemake.yaml
@@ -21,14 +21,15 @@ sqlite_select_command_sra : SELECT
                             LEFT JOIN SRA
                               ON SRABioSampleAccession = BioSampleAccession
                             WHERE
-                              BioSampleComment LIKE '%KEEP%SRA%Ancient%Placement%'
+                              (SRARunAccession = 'SRR1048902' OR
+                               SRARunAccession = 'SRR1048905')
 
 sqlite_select_command_local : SELECT
                               BioSampleAccession
                             FROM
                               BioSample
                             WHERE
-                              (BioSampleComment LIKE 'None')
+                              (BioSampleComment LIKE '%Local%Test%')
 
 sqlite_select_command_ref : SELECT
                               AssemblyFTPGenbank
@@ -40,10 +41,12 @@ sqlite_select_command_ref : SELECT
                               (BioSampleComment LIKE '%Assembly%Modern%Reference%')
 
 # Dataset size
-max_datasets_assembly : 1000
-max_datasets_sra : 1000
+max_datasets_assembly : 3
+max_datasets_sra : 2
 reads_origin :
   - "assembly"
+  - "sra"
+  - "local"
 
 # misc filtering
 detect_repeats_threshold : 90
@@ -53,7 +56,9 @@ reference_locus : "AL590842"
 reference_locus_name : "chromosome"
 reference_locus_start : "0"
 reference_locus_end : "4653728"
-reference_date : "-29"
+reference_date_bp : "29"
+reference_lat : "38.7251776"
+reference_lon : "-105.607716"
 
 # Eager param
 eager_rev: "2.2.1"
@@ -73,7 +78,7 @@ snippy_base_qual : 20
 snippy_map_qual : 30
 snippy_min_frac : 0.9
 snippy_mask_char : "X"
-snippy_missing_data : 5
+snippy_missing_data : 50
 snippy_snp_density : 10
 # Make this an empty string if removing singletons
 #snippy_keep_singleton: ""
@@ -90,13 +95,18 @@ snippy_multi_plot_missing_data:
 iqtree_model: "-m MFP"
 #iqtree_model : "-m K3Pu+F+I"
 iqtree_seed : "674947425" # keeping it consistent in a config file allows for checkpointing
+
 # Outgroup Option #1: Reference
-#iqtree_outgroup : "Reference"
+iqtree_outgroup : "Reference"
+
 # Outgroup Option #2: Basal modern clade
-iqtree_constraint: "((GCA_000323485.1_ASM32348v1_genomic,GCA_000323845.1_ASM32384v1_genomic),Reference);"
-iqtree_outgroup : "GCA_000323485.1_ASM32348v1_genomic,GCA_000323845.1_ASM32384v1_genomic"
+#iqtree_outgroup : "GCA_000323485.1_ASM32348v1_genomic"
+
 # Outgroup Option #3: Basal ancient clade
-#iqtree_constraint: "((SAMEA3541826,SAMEA3541827),Reference);"
 #iqtree_outgroup : "SAMEA3541826,SAMEA3541827"
-iqtree_other : ""
+
+# Outgroup Option #4: Other species
+#iqtree_outgroup : "GCA_900637475.1_51108_B01_genomic,GCA_000834295.1_ASM83429v1_genomic"
+
+iqtree_other : "--ufboot 1000"
 iqtree_runs : 1