Determine Shigella serotype from assemblies or Illumina paired-end reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
seqs{:bash}
:file
Assembly or paired-end Illumina reads
*.{fasta,fasta.gz,fastq.gz}
tsv{:bash}
*.tsv{:bash}
A TSV formatted file with ShigEiFinder results
*.tsv
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
