Description

Determine Shigella serotype from assemblies or Illumina paired-end reads

Input

name:type
description
pattern

meta:map

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

]

seqs:file

Assembly or paired-end Illumina reads

*.{fasta,fasta.gz,fastq.gz}

Output

name:type
description
pattern

tsv

meta:map

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

]

*.tsv:file

A TSV formatted file with ShigEiFinder results

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

shigeifinder
GPL v3

Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies