Prune BGCFlow rules

[matinnuhamunada]

I think we should reduce the number of rules, either by:

• Dropping unused or redundant rules
• Merging relevant rules into one package

These are the rules that are currently available:

Rules	Notebook / Markdown Report	Drop / Merge	Comments
mlst
eggnog
refseq-masher
mash
fastani
automlst-wrapper
roary
eggnog-roary
seqfu
rnammer
bigslice
query-bigslice
checkm
gtdbtk
prokka-gbk
antismash
arts
diamond
diamond-roary
deeptfactor
deeptfactor-roary
cblaster-genome
cblaster-bgc
patric_meta
bigscape

[OmkarSaMo]

Please find my comments below

Rules	Notebook / Markdown Report	Drop / Merge	Comments
mlst	Not needed	Drop	Only useful for pathogenic bacteria and slowly we are moving towards genome based classification anyway
eggnog	Useful for some smaller projects	Keep for some projects	Low priority as eggnog-roary is more useful. Table with genome_id as index and COG categories as columns with the number of genes in COG per genome as values. The visuals for each genome, when clicked on the table index, can include bar chart COG category counts spread across the genome (use buckets of 100 genes) PFA the visual no 1
refseq-masher	Not needed	Drop	Stopped using since the DB is quite old
mash	Very useful	Keep it as pimary	Hierarchical clustering image and MASH distance heatmap as visuals. Bar chart with number of genomes per Mash cluster. Table with mash cluster assignment for each genome.
fastani	Useful	Optional secondary	Use MASH distance as primary report as its faster. Hierarchical clustering image and FastANI distance heatmap as visuals. Bar chart with number of genomes per FastANI cluster. Table with FastANI cluster assignment for each genome.
automlst-wrapper	Useful	Keep	Downloadable tree file in newick. Possibly include extra tables that can be used in iTOL with documentation steps.
roary	Very useful	Keep	Visuals can include pangenome curve, gene presence heatmap, table with gene presence binary, table with gene presence locus_tags, table with list of genes in the pangenome, Link to Eggnog-roary report
eggnog-roary	Very useful	Keep	Visuals with pangenome category bar chart per COG category, table with eggnog annotations for each gene in pangenome (expansion of roary pagenome annotation table), Link to roary report
seqfu	Very useful	Keep	Existing visuals and tables are great
rnammer	Drop
bigslice	Keep
query-bigslice	Keep
checkm	Useful
gtdbtk	Keep
prokka-gbk	Make default
antismash	Keep
arts	Dev?
diamond	Drop		Download database and give example how to use
diamond-roary	Drop	Low priority	Visuals can include bar chart of TFs predicted in each category of pangenome. Need to brainstorm for visuals.
deeptfactor	Drop	Low priority	Visuals can include histogram of TFs predicted per genome. Need to brainstorm for visuals.
deeptfactor-roary	Drop	Low priority	Visuals can include bar chart of TFs predicted in each category of pangenome. Need to brainstorm for visuals.
cblaster-genome	Keep	Low priority	Can include link to download blastdb
cblaster-bgc	Drop l	Low priority	Can include link to download blastdb
patric_meta	Drop	Drop	Maybe use NCBI metadata instead, I had hard time to link every genome to PATRIC correctly
bigscape	Very important	Keep	Provide more tables that can be loaded to Cytoscape. Add table with genome metadata on number of Known BGCs, unique BGCs, etc., Add GCF presence heatmap or table.

Example visual:

1. Eggnog notebook visual per genome page