Nextflow Registry | nf-core/instrain/compare@0.0.0-6c4ed3a

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

Strain-level comparisons across multiple inStrain profiles

instrain compare align diversity coverage

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @margotl9 @CarsonJM

Maintainers: @margotl9 @CarsonJM

Strain-level comparisons across multiple inStrain profiles

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

include { INSTRAIN_COMPARE } from 'nf-core/instrain/compare'

MIT License

Process

`Name`	`INSTRAIN_COMPARE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bams` file	Path to .bam files that were profiled `*.{bam,sam}`
`profiles` directory	InStrain profile folders `*.IS/`

`stb_file` file	Path to .stb (scaffold to bin) file that was profiled `*.stb`

Output 6 channels

#1 compare tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.IS_compare` directory	inStrain compare folders `*.IS_compare/`

#2 snv_info tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`.IS_compare/output/.IS_compare_pooled_SNV_info.tsv` file	SNV information `*.tsv`

#3 snv_keys tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`.IS_compare/output/.IS_compare_pooled_SNV_data_keys.tsv` file	SNV keys `*.tsv`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 pooled_snv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`.IS_compare/output/.IS_compare_pooled_SNV_data.tsv` file	Pooled SNV `*.tsv`

#6 comparisons_table tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`.IS_compare/output/.IS_compare_comparisonsTable.tsv` file	Comparisons table `*.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 15:25:04 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Finstrain%2Fcompare/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/instrain/compare/blobs/sha256:c2927cbc9621daeef8f5e7d9ceb5984848b1bf6a68aaffa8d2e5b1281847fa72
Size	3.0 KB
Checksum	sha256:c2927cbc9621daeef8f5e7d9ceb5984848b1bf6a68aaffa8d2e5b1281847fa72
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:25:04 (UTC)		3	3.0 KB
0.0.0-3fc6d40	22 Apr 20