Use k-mers to rapidly subtype S. enterica genomes
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
seqs
:file
FASTA or FASTQ
*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}
scheme_metadata
Scheme subtype metadata table
*.{tab,tsv,txt}
summary
${prefix}-summary.txt
Tab-delimited subtyping summary output
*summary.txt
kmer_results
${prefix}-kmer-results.txt
Tab-delimited subtyping kmer matching output
*kmer-results.txt
simple_summary
${prefix}-simple-summary.txt
A simple version of summary output
*simple-summary.txt
versions_biohansel
${task.process}
:string
The name of the process
biohansel
The name of the tool
hansel --version 2>&1 | sed 's/^.*hansel //'
:eval
The expression to obtain the version of the tool
versions
Subtype Salmonella enterica genomes using 33bp k-mer typing schemes.
