Description

Salmonella serotype prediction from reads and assemblies

Input

name:type
description
pattern

meta:map

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

]

seqs:file

FASTQ or FASTA formated sequences

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

Output

name:type
description
pattern

log

meta:map

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

]

results/*_log.txt:file

A log of serotype antigen results

*_log.txt

tsv

meta:map

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

]

results/*_result.tsv:file

Tab-delimited summary of the SeqSero2 results

*_result.tsv

txt

meta:map

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

]

results/*_result.txt:file

Detailed summary of the SeqSero2 results

*_result.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

seqsero2
GPL v2

Salmonella serotype prediction from genome sequencing data