nf-core/genotyphi/parse @ 0.0.0-6c4ed3a
Summary
Genotype Salmonella Typhi from Mykrobe results
Get started
Add the following snippet to your workflow script to include this module.
include { GENOTYPHI_PARSE } from 'nf-core/genotyphi/parse'
License
MIT License
Process
Name
|
GENOTYPHI_PARSE |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
json
file
|
JSON formatted file of Mykrobe results *.json
|
Output
2 channels
#1
tsv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tsv
file
|
A tab-delimited file of predicted genotypes *.tsv
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| genotyphi | Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome) | https://github.com/katholt/genotyphi |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:21:12 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgenotyphi%2Fparse/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/genotyphi/parse/blobs/sha256:798bae543c57fdbcbf5a7bfa6ceb40def32f1796cb16159b03c613c2fb4a5c13 |
| Size | 2.3 KB |
| Checksum | sha256:798bae543c57fdbcbf5a7bfa6ceb40def32f1796cb16159b03c613c2fb4a5c13 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:21:12 (UTC) | 3 | 2.3 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:13:47 (UTC) | 3 | 2.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:05:48 (UTC) | 3 | 2.3 KB |