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

nf-core/alignoth @ 0.0.0-0c7146d

Creating alignment plots from bam files

genomics alignment visualization pileup plotting

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @famosab

Maintainers: @famosab

Creating alignment plots from bam files

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

include { ALIGNOTH } from 'nf-core/alignoth'

MIT License

Process

`Name`	`ALIGNOTH`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Sorted BAM/CRAM/SAM file to be visualized `*.{bam,cram,sam}`
`bai` file	Index file for the BAM/CRAM/SAM file `*.{bai,crai}`
`fasta` file	Reference fasta file `*.{fa,fasta}`
`fai` file	Index file for the reference fasta file `*.{fa,fasta}.fai`
`bed` file	Bed file with regions to be visualized (optional) `*.bed`
`vcf` file	VCF file with variants to be highlighted (optional) `*.vcf`
`tbi` file	Index file for the VCF file `*.vcf.tbi`

Output 4 channels

#1 html tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.html` file	HTML file with the alignment plot `*.html`

#2 output tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}` directory	Output directory with the alignment plot and all intermediate files `*`

#3 vl_json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.vl.json` file	Vega-Lite JSON file with the alignment plot `*.vl.json`

#4 versions_alignoth tuple

`${task.process}` string	The name of the process
`alignoth` string	The name of the tool
`alignoth --version \| sed 's/alignoth //g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
alignoth	A tool for creating alignment plots from bam files.	https://github.com/alignoth/alignoth/blob/v1.4.6/README.md

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:42:00 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Falignoth/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/alignoth/blobs/sha256:d1c8371742a9f29f140418284d3bfc24e305502e81c3bfb528c41c04a26077ca
Size	3.6 KB
Checksum	sha256:d1c8371742a9f29f140418284d3bfc24e305502e81c3bfb528c41c04a26077ca
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:01:57 (UTC)		3	3.6 KB
0.0.0-0c7146d	08 Apr 2026 18:42:00 (UTC)