Description

Functional annotation of phages

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

phage_fasta:file

A FASTA file containing phage sequence(s)

*.{fasta,fna,fa}

pharokka_db:file

Directory containing Pharokka’s database

Output

name:type
description
pattern

cds_final_merged_output

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv:file

A file containing the final merged output of CDSs

*_cds_final_merged_output.tsv

cds_functions

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_cds_functions.tsv:file

A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs

*_cds_functions.tsv

length_gc_cds_density

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv:file

A file containing the length, GC content, and CDS density of the phage genome

*_length_gc_cds_density.tsv

card

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_top_hits_card.tsv:file

OPTIONAL - A file containing any CARD database hits

*top_hits_card.tsv

vfdb

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv:file

OPTIONAL - A file containing any VFDB database hits

*top_hits_vfdb.tsv

mash

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv:file

OPTIONAL - File containing top hits to INPHARED database

*_top_hits_mash_inphared.tsv

reoriented

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta:file

OPTIONAL - FASTA file reoriented to start with the large terminase subunit

*_genome_terminase_reoriented.fasta

versions

versions.yml:file

File containing software versions

versions.yml