Region: Rebase Emma's changes
This commit rebases changes from and
@@ -7,16 +7,22 @@ def get_todays_date():
date = datetime.today().strftime('%Y-%m-%d')
return date
+# Add new regions here!
REGIONS = ["_North-America", "_Europe", ""]
wildcard_constraints:
- region="|_North-America|_Europe",
+ region = "|".join(REGIONS), # "|_North-America|_Europe"
date = "[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]"
# How to run: if no region is specified, it'll run a subsampled global build (200 per division)
# If a region is selected, it'll do 200/division for that region, and 20/division in the rest of the world
# -- preferentially sequences near the focal sequences
#
+# To run a regional build, be sure to update it to the list on line 10!
+#
+# You can run all builds in parallel!
+# snakemake -s Snakefile_Regions --cores 2 all_regions
+#
# You can use the specific rules below to call the whole build.
# Be sure to specify the 'additional' snakefile when you call, like so:
# snakemake -s Snakefile_Regions --cores 2 all_regions (all builds)
@@ -275,6 +281,7 @@ rule refine:
output:
tree = "results/tree{region}.nwk",
node_data = "results/branch_lengths{region}.json"
+ threads: 1
params:
root = "Wuhan-Hu-1/2019 Wuhan/WH01/2019",
clock_rate = 0.0008,
