Nextflow Registry | nf-core/shigapass@0.0.0-3fc6d40

nf-core/shigapass @ 0.0.0-3fc6d40

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: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:31:04 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fshigapass/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/shigapass/blobs/sha256:0f435fa9bc2c03279af2998c9e752daba8376d23fa552658b4785bc6e4644ff3
Size	2.7 KB
Checksum	sha256:0f435fa9bc2c03279af2998c9e752daba8376d23fa552658b4785bc6e4644ff3
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:45:13 (UTC)	3	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:31:04 (UTC)	3	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:37:41 (UTC)	3	2.7 KB