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nf-core/sistr @ 0.0.0-3fc6d40

Serovar prediction of salmonella assemblies

bacteria fasta salmonella
Latest version: 0.0.0-cd0ad38
Total downloads: 0
Source: nf-core/modules
Authors: @rpetit3
Maintainers: @rpetit3

Summary

Serovar prediction of salmonella assemblies

Get started

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

include { SISTR } from 'nf-core/sistr'

License

MIT License

Process
Name SISTR
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
fasta file

Nucleotide or protein sequences in FASTA format

 *.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}
Output 5 channels
#1 tsv tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.tab file

SISTR serovar prediction

 *.{tsv}
#2 cgmlst_csv tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*-cgmlst.csv file

CSV file destination for cgMLST allelic profiles

 *.{csv}
#3 allele_json tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*-allele.json file

Allele sequences and info to JSON

 *.{json}
#4 allele_fasta tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*-allele.fasta file

FASTA file destination of novel cgMLST alleles

 *.{fasta}
#5 versions_sistr tuple
${task.process} string

The name of the process
sistr string

The name of the tool
sistr --version 2>&1 | sed "s/^.*sistr_cmd //; s/ .*\$//" eval

The expression to obtain the version of the tool
Tool Description Homepage
sistr Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction https://github.com/phac-nml/sistr_cmd
Version 0.0.0-3fc6d40
Commit ID cd0ad387832473916b1f1c80c2ca673a7883bf94
Release Date 22 Apr 2026 15:31:54 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fsistr/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sistr/blobs/sha256:9908bd76fb014a8a29ef8087c872a5da53915bf879c835cb410c4a6e286658a9
Size 2.7 KB
Checksum sha256:9908bd76fb014a8a29ef8087c872a5da53915bf879c835cb410c4a6e286658a9
Downloads 0
Version Date Status Downloads Size Diff
0.0.0-cd0ad38 19 May 2026 15:01:45 (UTC) 0 2.8 KB ↔
0.0.0-6c4ed3a 23 Apr 2026 15:46:15 (UTC) 0 2.6 KB ↔
0.0.0-3fc6d40 22 Apr 2026 15:31:54 (UTC) 0 2.7 KB ↔
0.0.0-0c7146d 08 Apr 2026 19:38:04 (UTC) 0 2.6 KB -