Determine Shigella serotype from Illumina or Oxford Nanopore reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, is_ont:false ]
reads{:bash}
:file
Illumina or Nanopore FASTQ file
*.fastq.gz
tsv{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
${prefix}.tsv{:bash}
A TSV formatted file with ShigaTyper results
*.tsv
hits{:bash}
${prefix}-hits.tsv{:bash}
A TSV formatted file with individual gene hits
*-hits.tsv
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Typing tool for Shigella spp. from WGS Illumina sequencing
