Determine Shigella serotype from Illumina or Oxford Nanopore reads
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
Illumina or Nanopore FASTQ file
*.fastq.gz
tsv
${prefix}.tsv
A TSV formatted file with ShigaTyper results
*.tsv
hits
${prefix}-hits.tsv
A TSV formatted file with individual gene hits
*-hits.tsv
versions_shigatyper
${task.process}
:string
The name of the process
shigatyper
The name of the tool
shigatyper --version | sed 's/ShigaTyper //'
:eval
The expression to obtain the version of the tool
versions
Typing tool for Shigella spp. from WGS Illumina sequencing
