Functional annotation of phages
meta
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
phage_fasta
A FASTA file containing phage sequence(s)
*.{fasta,fna,fa}
pharokka_db
Directory containing Pharokka’s database
log
Log file containing all logging output
*.log
cds_functions
A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs
*_cds_functions.tsv
card
OPTIONAL - A file containing any CARD database hits
*top_hits_card.tsv
vfdb
OPTIONAL - A file containing any VFDB database hits
*top_hits_vfdb.tsv
mash
OPTIONAL - File containing top hits to INPHARED database
*_top_hits_mash_inphared.tsv
reoriented
OPTIONAL - FASTA file reoriented to start with the large terminase subunit
*_genome_terminase_reoriented.fasta
versions
File containing software versions
versions.yml
Fast Phage Annotation Program
