nf-core/biohansel @ 0.0.0-0c7146d
Summary
Use k-mers to rapidly subtype S. enterica genomes
Get started
Add the following snippet to your workflow script to include this module.
include { BIOHANSEL } from 'nf-core/biohansel'
License
MIT License
Process
Name
|
BIOHANSEL |
|---|
Input
2 channels
#1
tuple
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
file
|
Scheme subtype metadata table *.{tab,tsv,txt}
|
|---|
Output
4 channels
#1
summary
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}-summary.txt
file
|
Tab-delimited subtyping summary output *summary.txt
|
#2
kmer_results
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}-kmer-results.txt
file
|
Tab-delimited subtyping kmer matching output *kmer-results.txt
|
#3
simple_summary
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}-simple-summary.txt
file
|
A simple version of summary output *simple-summary.txt
|
#4
versions_biohansel
tuple
${task.process}
string
|
The name of the process |
|---|---|
biohansel
string
|
The name of the tool |
hansel --version 2>&1 | sed 's/^.*hansel //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| biohansel | Subtype Salmonella enterica genomes using 33bp k-mer typing schemes. | https://github.com/phac-nml/biohansel |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:26:58 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbiohansel/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/biohansel/blobs/sha256:b61e5f07413a3b038f9e88cd985dd48c3a83993c1e1b64b5103e46a6efe54189 |
| Size | 3.4 KB |
| Checksum | sha256:b61e5f07413a3b038f9e88cd985dd48c3a83993c1e1b64b5103e46a6efe54189 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:26:58 (UTC) | 1 | 3.4 KB | - |