Update gust

gust

@@ -32,6 +32,7 @@ if [[ -z "$2" ]]; then
         echo "and outgroup genomes, then run gust again. You can also modify"
         echo "parameters before running."
         cat <<EOF >config.yml
+#
 #=======================================================#
 #                     gust config file                  #
 #  most of this file is comments, which you can delete  #
@@ -52,15 +53,16 @@ bwa_parameters: "-a -k 19"
 # -a outputs all alignments
 # -k 19 is a kmer size of 19
 
-freebayes_parameters: "-C 2 --min-coverage 5 --standard-filter --ploidy 1"
-# -C 2 means at least 2 samples need to have alt alleles for a site to be kept
+freebayes_parameters: "-C 1 --min-coverage 5 --standard-filter --ploidy 1"
+# -C 1 means at least 1 sample needs to have alt allele for a site to be kept
 # --min-coverage 5 means at least 5 aligments to score a site
-# --standard-filter is to add more stringency
+# --standard-filter is equivalent to -m 30 -q 20 -R 0 -S 0
 # --ploidy 1 because these are typically haploid assemblies
 
 window_size: 50000
+sites_per_window: 10
 # window size in base pairs for LD pruning snp data
-# bigger window = fewer snps
+# number of sites to keep per window
 
 musclev5_parameters: "-replicates 100"
 # if runtime is important, you may want to reduce replicates
@@ -69,10 +71,10 @@ raxml_model: "GTR+G"
 # the phylogenetic model you would like to use see for options:
 # https://isu-molphyl.github.io/EEOB563/computer_labs/lab4/models.html
 
-raxml_parameters: "--bs-trees 100 --tree pars\{25\},rand\{25\} -brlen scaled"
+raxml_parameters: '--bs-trees 100 --tree pars\{25\},rand\{25\} -brlen scaled'
 # --bs-trees 100 is 100 bootstrapped trees
 # --tree pars{25},rand{25} is to use 25 parsimonious trees and 25 random trees
-# the curly braces need to be escaped with \ for snakemake
+# the curly braces need to be escaped with \ for snakemake and note the single quotes
 # -brlen scaled is the model for branch linkage
 EOF
         exit 1