Description

Identify cap locus serotype and structure in your Haemophilus influenzae assemblies

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta:file

FASTA formatted assembly file

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}

database_dir:directory

Optional - Directory containing locus database

*/*

model_fp:file

Optional - Prodigal model to use for gene prediction

*.{bin}

Output

name:type
description
pattern

gbk

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.gbk:file

GenBank file and cap locus annotations

*.gbk

svg

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.svg:file

Visualization of annotated cap locus

*.svg

tsv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.tsv:file

Detailed summary of cap locus annotations

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

hicap
GPL v3

In silico typing of the H. influenzae capsule locus