Core SNPs are identified by snippy-core. gubbins is used to identify and filter recombinant loci.
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.
--snippy_dirs:--ref: A reference.fastafile
nextflow run BCCDC-PHL/snippy-phylogenomics-nf \
--snippy_dirs </path/to/snippy_output_dirs> \
--ref ref.fa \
[--mask mask.bed] \
--outdir outdir