Nextflow Registry | nf-core/abra2@0.0.0-0c7146d

nf-core/abra2 @ 0.0.0-0c7146d

Assembly Based ReAligner for next-generation sequencing data

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @adamrtalbot

Maintainers: @adamrtalbot

Assembly Based ReAligner for next-generation sequencing data

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

include { ABRA2 } from 'nf-core/abra2'

MIT License

Process

`Name`	`ABRA2`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bams` file	Input BAM file - must be coordinate sorted `*.bam`
`bais` file	BAM index file `*.bai`

#2 tuple

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

#3 tuple

`meta3` map	Groovy Map containing reference index information e.g. `[ id:'genome' ]`
`fai` file	Reference genome FASTA index file `*.{fai}`

#4 tuple

`meta4` map	Groovy Map containing target regions information e.g. `[ id:'targets' ]`
`targets` file	BED file containing target regions for realignment (optional) `*.{bed}`

#5 tuple

`meta5` map	Groovy Map containing GTF annotation information e.g. `[ id:'annotation' ]`
`gtf` file	GTF annotation file for RNA-seq data (optional) `*.{gtf}`

#6 tuple

`meta6` map	Groovy Map containing known indels information e.g. `[ id:'known_indels' ]`
`known_indels` file	VCF file containing known indels (optional) `*.{vcf,vcf.gz}`

Output 3 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bam.bai` file	BAM index file (optional) `*.abra.bam.bai`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.bam` file	Realigned BAM file `*.abra.bam`

#3 versions_abra2 tuple

`${task.process}` string	The name of the process
`abra2` string	The name of the tool
`abra2 2>&1 \| sed -n 's/.*Abra version: //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
abra2	Assembly Based ReAligner for next-generation sequencing data	https://github.com/mozack/abra2

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:20:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fabra2/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/abra2/blobs/sha256:21a75bb72c4f6344775c5b86497f81a96dbec5d915b96bf90f26edcc4dc2a515