fix

n_t/Snakefile

@@ -49,11 +49,26 @@ num_sampled_genomes_per_replicate = config["num_sampled_genomes_per_replicate"]
 # Here is a list of sample sizes to run msmc on. 
 # Each element counts as its own analysis
 # so there will be "replicates" runs for each size
+#
+# and a similar setup for SMCSMC
 num_sampled_genomes_msmc = [int(x) for x in config["num_sampled_genomes_msmc"].split()]
+num_sampled_genomes_smcsmc = [int(x) for x in config["num_sampled_genomes_smcsmc"].split()]
 
 # The number of msmc Baumwelch(?) iterations to run,
 # typically 20
+#
+# And again, similar for SMCSMC. Number of stochastic EM iterations.
+# 15 is typical, but more is good too. Assess for convergence based on 
+# rainbow plots.
 num_msmc_iterations = config["num_msmc_iterations"]
+num_smcsmc_iterations = config["num_smcsmc_iterations"]
+
+# Number of particles to use for SMCSMC
+# 
+# A good starting point is 50k, and see if reducing 
+# significantly impacts the estimates that you are
+# recieveing. 
+num_smcsmc_particles = config["num_smcsmc_particles"]
 
 # The number of replicates of each analysis you would like to run
 replicates = config["replicates"]
@@ -72,12 +87,11 @@ model = model_class()
 genetic_map_class = getattr(species,config["genetic_map"])
 genetic_map = genetic_map_class()
 
-# A list containing the names all simulated chromosomes you would 
-# like to include in each analysis
-# TODO: Change this to list(species.genome.chromosomes)
+# The names of all chromosomes to simulate, separated by commas
+# Use "all" to simulate all chromsomes for the genome
 chrm_list = [chrom for chrom in species.genome.chromosomes]
 if(config["chrm_list"] != "all"):
-    chrm_list = chrm_list[:config["chrm_list"]]
+    chrm_list = [chr for chr in config["chrm_list"].split(",")]
 
 # For plotting
 generation_time = config["generation_time"]
@@ -154,7 +168,7 @@ rule run_stairwayplot:
         stairwayplot_code,
     output: output_dir + "/Results/{seeds}/stairwayplot_estimated_Ne.txt"
     threads: 20
-    run: 
+    run:
         inputs = expand(output_dir + "/Intermediate/{seeds}/{chrms}.trees",
             seeds=wildcards.seeds, chrms=chrm_list)
         runner = stairway.StairwayPlotRunner(

n_t/readme.md

@@ -38,7 +38,6 @@ might look like this:
 
 ```json
 {
-<<<<<<< HEAD
 	"seed" : 12345,
 	"population_id" : 0,
 	"num_sampled_genomes_per_replicate" : 20,