Nextflow Registry | nf-core/viralconsensus@0.0.0-6c4ed3a

nf-core/viralconsensus @ 0.0.0-6c4ed3a

Fast and memory-efficient viral consensus genome sequence generation from read alignments

virus genomics consensus bam fasta

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @niemasd

Maintainers: @niemasd @lucaspatel

Fast and memory-efficient viral consensus genome sequence generation from read alignments

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

include { VIRALCONSENSUS } from 'nf-core/viralconsensus'

MIT License

Process

`Name`	`VIRALCONSENSUS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM/SAM/CRAM file containing aligned reads `*.{bam,sam,cram}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'sarscov2' ]
`fasta` file	Reference genome sequence in FASTA format `*.{fa,fasta,fna}`

`primer_bed` file	Optional BED file with primer coordinates for trimming `*.bed`

`save_pos_counts` boolean	Save per-position counts to a TSV file

`save_ins_counts` boolean	Save insertion counts to a JSON file

Output 4 channels

#1 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.consensus.fa` file	Consensus genome sequence in FASTA format `*.consensus.fa`

#2 ins_counts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ins_counts.json` file	Insertion counts (optional, enabled via save_ins_counts input) `*.ins_counts.json`

#3 pos_counts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pos_counts.tsv` file	Per-position base counts (optional, enabled via save_pos_counts input) `*.pos_counts.tsv`

#4 versions_viralconsensus tuple

`${task.process}` string	The process the versions were collected from
`viralconsensus` string	The tool name
`viral_consensus --version \| sed 's/.*v//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
viralconsensus	ViralConsensus is a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.	https://github.com/niemasd/ViralConsensus

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:52:36 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fviralconsensus/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/viralconsensus/blobs/sha256:186f32b7c7dc7ff281f45437d07f0bd1b02cf539946f75e5f9d4319c1cea72a1
Size	3.2 KB
Checksum	sha256:186f32b7c7dc7ff281f45437d07f0bd1b02cf539946f75e5f9d4319c1cea72a1
Downloads	5

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:52:36 (UTC)		5	3.2 KB
0.0.0-3fc6d40