Nextflow Registry | nf-core/ivar/variants@0.0.0-0c7146d

nf-core/ivar/variants @ 0.0.0-0c7146d

Call variants from a BAM file using iVar

amplicon sequencing variants fasta

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @andersgs @drpatelh

Maintainers: @andersgs @drpatelh

Call variants from a BAM file using iVar

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

include { IVAR_VARIANTS } from 'nf-core/ivar/variants'

MIT License

Process

`Name`	`IVAR_VARIANTS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	A sorted (with samtools sort) and trimmed (with iVar trim) bam file `*.bam`

`fasta` file	The reference sequence used for mapping and generating the BAM file `*.fa`

`fai` file	The index for the reference sequence used for mapping and generating the BAM file `*.fai`

`gff` file	A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. `*.gff`

`save_mpileup` boolean	Save mpileup file generated by ivar variants `*.mpileup`

Output 3 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tsv` file	iVar generated TSV file with the variants `*.tsv`

#2 mpileup tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.mpileup` file	mpileup output from samtools mpileup [OPTIONAL] `*.mpileup`

#3 versions

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

Tool	Description	Homepage
ivar	iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.	https://github.com/andersen-lab/ivar

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:49:41 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fivar%2Fvariants/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ivar/variants/blobs/sha256:2dfedbadd453fe9b01aa3ec04c6898a539c38bf45d65b86defeb213f311f372d
Size	2.9 KB
Checksum	sha256:2dfedbadd453fe9b01aa3ec04c6898a539c38bf45d65b86defeb213f311f372d
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:49:41 (UTC)		1	2.9 KB	-