Nextflow Registry | nf-core/viralconsensus@0.0.0-0c7146d

nf-core/viralconsensus @ 0.0.0-0c7146d

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

virus genomics consensus bam fasta

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:22:45 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fviralconsensus/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/viralconsensus/blobs/sha256:e66de2d00ce83f1ef9014a7808c43561f796130bea7db1f5e52dd824e0f21bd3
Size	3.1 KB
Checksum	sha256:e66de2d00ce83f1ef9014a7808c43561f796130bea7db1f5e52dd824e0f21bd3
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:22:45 (UTC)		1	3.1 KB	-