Undo defaults.yaml change, use one config per build, add default profile

Snakefile

@@ -11,10 +11,6 @@ if version.parse(augur_version) < version.parse(min_augur_version):
     sys.exit(1)
 
 
-# Use default configuration values. Override with Snakemake's --configfile/--config options.
-configfile: "config/defaults.yaml"
-
-
 build_dir = "results"
 
 

config/config_hmpxv1.yaml

@@ -1,5 +1,18 @@
+exclude: "config/exclude_accessions_mpxv.txt"
+reference: "config/reference.fasta"
+genemap: "config/genemap.gff"
+genbank_reference: "config/reference.gb"
 colors: "config/colors_hmpxv1.tsv"
+clades: "config/clades.tsv"
+lat_longs: "config/lat_longs.tsv"
 auspice_config: "config/auspice_config_hmpxv1.json"
+description: "config/description.md"
+tree_mask: "config/tree_mask.tsv"
+
+# Use `accession` as the ID column since `strain` currently contains duplicates¹.
+# ¹ https://github.com/nextstrain/monkeypox/issues/33
+strain_id_field: "accession"
+display_strain_field: "strain"
 
 build_name: "hmpxv1"
 auspice_name: "mpox_mpxv-IIb"
@@ -58,6 +71,9 @@ root: "MK783032 MK783030"
 clock_rate: 5.7e-5
 clock_std_dev: 2e-5
 
+## recency
+recency: true
+
 mask:
   from_beginning: 800
   from_end: 6422

config/config_hmpxv1_big.yaml

@@ -1,5 +1,18 @@
+exclude: "config/exclude_accessions_mpxv.txt"
+reference: "config/reference.fasta"
+genemap: "config/genemap.gff"
+genbank_reference: "config/reference.gb"
 colors: "config/colors_hmpxv1.tsv"
+clades: "config/clades.tsv"
+lat_longs: "config/lat_longs.tsv"
 auspice_config: "config/auspice_config_hmpxv1_big.json"
+description: "config/description.md"
+tree_mask: "config/tree_mask.tsv"
+
+# Use `accession` as the ID column since `strain` currently contains duplicates¹.
+# ¹ https://github.com/nextstrain/monkeypox/issues/33
+strain_id_field: "accession"
+display_strain_field: "strain"
 
 build_name: "hmpxv1_big"
 auspice_name: "mpox_mpxv-IIb-B.1"
@@ -36,6 +49,9 @@ root: "OP890401"
 clock_rate: 5.7e-5
 clock_std_dev: 2e-5
 
+## recency
+recency: true
+
 mask:
   from_beginning: 800
   from_end: 6422

config/config_mpxv.yaml

@@ -1,5 +1,18 @@
+exclude: "config/exclude_accessions_mpxv.txt"
+reference: "config/reference.fasta"
+genemap: "config/genemap.gff"
+genbank_reference: "config/reference.gb"
 colors: "config/colors_mpxv.tsv"
+lat_longs: "config/lat_longs.tsv"
 auspice_config: "config/auspice_config_mpxv.json"
+description: "config/description.md"
+clades: "config/clades.tsv"
+tree_mask: "config/tree_mask.tsv"
+
+# Use `accession` as the ID column since `strain` currently contains duplicates¹.
+# ¹ https://github.com/nextstrain/monkeypox/issues/33
+strain_id_field: "accession"
+display_strain_field: "strain"
 
 build_name: "mpxv"
 auspice_name: "mpox_mpxv"
@@ -41,12 +54,22 @@ filter:
     group_by: "--group-by country year"
     sequences_per_group: "--subsample-max-sequences 100"
 
+## align
+max_indel: 10000
+seed_spacing: 1000
+
+## treefix
+fix_tree: true
+
 ## refine
 timetree: false
 root: "min_dev"
 clock_rate: 3e-6
 clock_std_dev: 6e-6
 
+## recency
+recency: true
+
 mask:
   from_beginning: 1350
   from_end: 6422

profiles/default/config.yaml

@@ -0,0 +1,5 @@
+cores: all
+printshellcmds: true
+reason: true
+rerun-incomplete: true
+configfile: config/config_mpxv.yaml