Nextflow Registry | nf-core/genotyphi/parse@0.0.0-0c7146d

nf-core/genotyphi/parse @ 0.0.0-0c7146d

Genotype Salmonella Typhi from Mykrobe results

genotype Salmonella Typhi Mykrobe

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @rpetit3

Maintainers: @rpetit3

Genotype Salmonella Typhi from Mykrobe results

Add the following snippet to your workflow script to include this module.

include { GENOTYPHI_PARSE } from 'nf-core/genotyphi/parse'

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:44:12 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgenotyphi%2Fparse/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/genotyphi/parse/blobs/sha256:5300c01807da9ff06b700ab359a5f10cd81aec3f6c8ee45f88bb52664137b0c8
Size	2.3 KB
Checksum	sha256:5300c01807da9ff06b700ab359a5f10cd81aec3f6c8ee45f88bb52664137b0c8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:44:12 (UTC)		1	2.3 KB	-