In silico prediction of E. coli serotype
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta
:file
FASTA formatted assembly file
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}
log
*.log
ectyper log output
tsv
*.tsv
ectyper serotyping results in TSV format
txt
*.txt
Allele report generated from BLAST results
versions_ectyper
${task.process}
:string
The name of the process
ectyper
The name of the tool
ectyper --version 2>&1 | sed 's/.*ectyper //; s/ .*$//'
:eval
The expression to obtain the version of the tool
versions
ECtyper is a python program for serotyping E. coli genomes
