Update README.md (#11)

README.md

@@ -2,6 +2,34 @@
 
 Core SNPs are identified by `snippy-core`. [`gubbins`](https://github.com/nickjcroucher/gubbins) is used to identify and filter recombinant loci.
 
+
+```mermaid
+flowchart TD
+  snippy_dirs[snippy_dirs] --> snippy_core[snippy_core]
+  ref[reference.fasta] --> snippy_core
+  snippy_core --> core_aln[core.aln]
+  snippy_core --> core_variants[core.vcf]
+  snippy_core --> core_stats[core.vcf]
+  snippy_core --> full_alignment[core.full.aln]
+  snippy_core --> clean_full_alignment[clean.full.aln]
+  clean_full_alignment -->|process WITH gubbins| gubbins(gubbins)
+  gubbins --> filtered_polymorphic_sites[gubbins.filtered_polymorphic_sites.fasta]
+  gubbins --> recombination_predictions_gff[gubbins.recombination_predictions.gff]
+  gubbins --> per_branch_statistics[gubbins.per_branch_statistics.tsv]
+  clean_full_alignment --> |process WITHOUT gubbins| snp_sites
+  snp_sites -->  snp_sites_out[clean.core.aln]
+  filtered_polymorphic_sites --> snp_sites
+  snp_sites_out --> iqtree
+  iqtree --> iqtree_out[alignment.treefile]
+  snp_sites_out --> snp_dists
+  snp_dists --> snp_dists_out[alignment.distances.tsv]
+  iqtree_out --> shiptv
+  shiptv --> tree_html[tree.html]  
+  
+```
+
+Note: the process WITHOUT gubbins occurs if --skip_gubbins is true, or if there are only two samples input as gubbins requires a minimum of 3 samples.
+
 ## Inputs
 
 - `--snippy_dirs`: