Nextflow Registry | nf-core/shigapass@0.0.0-0c7146d

nf-core/shigapass @ 0.0.0-0c7146d

ShigaPass is an in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.

bacteria shigella stec

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @maxlcummins

Maintainers: @maxlcummins

Summary

ShigaPass is an in silico tool used to predict Shigella serotypes and to differentiate between Shigella, EIEC (Enteroinvasive E. coli), and non Shigella/EIEC using assembled whole genomes.

Get started

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

include { SHIGAPASS } from 'nf-core/shigapass'

License

MIT License

Process

`Name`	`SHIGAPASS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	FASTA, GenBank or EMBL formatted file. Note that the standard input for ShigaPass is a file of file paths - here for paralellisation a fasta file is required. `*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}`

Output 3 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.tsv` file	Tab-delimited report of results `${prefix}.tsv`

#2 flex_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_ShigaPass_Flex_summary.tsv` file	Tab-delimited report of results `*_ShigaPass_Flex_summary.tsv`

#3 versions_shigapass tuple

`${task.process}` string	The process the versions were collected from
`shigapass` string	The tool name
`ShigaPass.sh -v 2>&1 \| sed 's/^.*ShigaPass version //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
shigapass	ShigaPass is an in silico tool used to predict Shigella serotypes	https://github.com/imanyass/ShigaPass

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:13:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fshigapass/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/shigapass/blobs/sha256:5f81bd796c901f92be4c88dc2c2b8c9cd1f4ca068b5b9687dc254192e6ae0798
Size	2.7 KB
Checksum	sha256:5f81bd796c901f92be4c88dc2c2b8c9cd1f4ca068b5b9687dc254192e6ae0798
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:13:49 (UTC)		1	2.7 KB	-