Nextflow Registry | nf-core/sentieon/bwamem@0.0.0-6c4ed3a

nf-core/sentieon/bwamem @ 0.0.0-6c4ed3a

Performs fastq alignment to a fasta reference using Sentieon's BWA MEM

mem bwa alignment map fastq bam sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200 @DonFreed

Performs fastq alignment to a fasta reference using Sentieon's BWA MEM

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

include { SENTIEON_BWAMEM } from 'nf-core/sentieon/bwamem'

MIT License

Process

`Name`	`SENTIEON_BWAMEM`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`reads` file	Genome fastq files (single-end or paired-end)

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`index` file	BWA genome index files `*.{amb,ann,bwt,pac,sa}`

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`fasta` file	Genome fasta file `*.{fa,fasta}`

#4 tuple

`meta4` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`fasta_fai` file	The index of the FASTA reference. `*.fai`

Output 3 channels

#1 bam_and_bai tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`${prefix}` file	BAM file with corresponding index. `*.{bam,bai}`
`${prefix}.{bai,crai}` file	BAM file with corresponding index. `*.{bam,bai}`

#2 versions_bwa tuple

`${task.process}` string	The process the versions were collected from
`bwa` string	The tool name
`sentieon bwa 2>&1 \| sed -n "s/^Version: *//p"` string	The command used to generate the version of the tool

#3 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool

Tool	Description	Homepage
sentieon	Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.	https://www.sentieon.com/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:43:53 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fbwamem/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/bwamem/blobs/sha256:6c40caaf3b4511c6b161d163642ac9bac44b0e961059ee744e4940a6d9459831
Size	4.0 KB
Checksum	sha256:6c40caaf3b4511c6b161d163642ac9bac44b0e961059ee744e4940a6d9459831
Downloads	4

Version	Date	Status	Downloads	Size