Functional annotation of phages
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
phage_fasta{:bash}
:file
A FASTA file containing phage sequence(s)
*.{fasta,fna,fa}
pharokka_db{:bash}
Directory containing Pharokka’s database
cds_final_merged_output{:bash}
${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv{:bash}
A file containing the final merged output of CDSs
*_cds_final_merged_output.tsv
cds_functions{:bash}
${prefix}_pharokka/${prefix}_cds_functions.tsv{:bash}
A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs
*_cds_functions.tsv
length_gc_cds_density{:bash}
${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv{:bash}
A file containing the length, GC content, and CDS density of the phage genome
*_length_gc_cds_density.tsv
card{:bash}
${prefix}_pharokka/${prefix}_top_hits_card.tsv{:bash}
OPTIONAL - A file containing any CARD database hits
*top_hits_card.tsv
vfdb{:bash}
${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv{:bash}
OPTIONAL - A file containing any VFDB database hits
*top_hits_vfdb.tsv
mash{:bash}
${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv{:bash}
OPTIONAL - File containing top hits to INPHARED database
*_top_hits_mash_inphared.tsv
reoriented{:bash}
${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta{:bash}
OPTIONAL - FASTA file reoriented to start with the large terminase subunit
*_genome_terminase_reoriented.fasta
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Fast Phage Annotation Program
