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nf-core/instrain/profile @ 0.0.0-6c4ed3a

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

instrain metagenomics population genomics profile
Latest version: 0.0.0-6c4ed3a
Total downloads: 8
Source: nf-core/modules
Authors: @mrolm
Maintainers: @mrolm

Summary

inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification

Get started

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

include { INSTRAIN_PROFILE } from 'nf-core/instrain/profile'

License

MIT License

Process
Name INSTRAIN_PROFILE
Input 4 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'test']
bam file

Path to .bam file to be profiled

 *.{bam,sam}
genome_fasta file

Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file

 *.{fasta,fna,fa}
genes_fasta file

Path to .fna file of genes to be profiled (OPTIONAL)

 *.{fasta,fna,fa}
stb_file file

Path to .stb (scaffold to bin) file to be profiled (OPTIONAL)

 *.stb
Output 8 channels
#1 snvs tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_SNVs.tsv file

SNVs

 *.tsv
#2 linkage tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_linkage.tsv file

Linkage information

 *.tsv
#3 profile tuple
meta map

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

InStrain profile folder

 *.IS/
#4 versions
versions.yml file

File containing software versions

 versions.yml
#5 gene_info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_gene_info.tsv file

Gene information

 *.tsv
#6 genome_info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_genome_info.tsv file

Genome information

 *.tsv
#7 mapping_info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_mapping_info.tsv file

Mapping information

 *.tsv
#8 scaffold_info tuple
meta map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
*.IS/output/*.IS_scaffold_info.tsv file

Scaffold information

 *.tsv
Tool Description Homepage
instrain Calculation of strain-level metrics https://github.com/MrOlm/instrain
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:25:05 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Finstrain%2Fprofile/0.0.0-6c4ed3a/download