nf-core/shigatyper @ 0.0.0-0c7146d
Summary
Determine Shigella serotype from Illumina or Oxford Nanopore reads
Get started
Add the following snippet to your workflow script to include this module.
include { SHIGATYPER } from 'nf-core/shigatyper'
License
MIT License
Process
Name
|
SHIGATYPER |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false, is_ont:false ] |
|---|---|
reads
file
|
Illumina or Nanopore FASTQ file *.fastq.gz
|
Output
3 channels
#1
tsv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}.tsv
file
|
A TSV formatted file with ShigaTyper results *.tsv
|
#2
hits
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}-hits.tsv
file
|
A TSV formatted file with individual gene hits *-hits.tsv
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| shigatyper | Typing tool for Shigella spp. from WGS Illumina sequencing | https://github.com/CFSAN-Biostatistics/shigatyper |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:13:51 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fshigatyper/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/shigatyper/blobs/sha256:8a4f8666ae9ab65ba89aabc0c72e5b3bb806dbb2d8c30d591e4e6d076a378af1 |
| Size | 2.5 KB |
| Checksum | sha256:8a4f8666ae9ab65ba89aabc0c72e5b3bb806dbb2d8c30d591e4e6d076a378af1 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:13:51 (UTC) | 1 | 2.5 KB | - |