Nextflow Registry | nf-core/sentieon/bwamem@0.0.0-0c7146d

nf-core/sentieon/bwamem @ 0.0.0-0c7146d

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

mem bwa alignment map fastq bam sentieon

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:11:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fbwamem/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sentieon/bwamem/blobs/sha256:9ab09fb592be363c0925880b13204fd7646c5ce8cefa2534c56638be8bc4391b
Size	3.9 KB
Checksum	sha256:9ab09fb592be363c0925880b13204fd7646c5ce8cefa2534c56638be8bc4391b
Downloads	1

Version	Date	Status	Downloads	Size	Diff