Nextflow Registry | nf-core/bwa/sampe@0.0.0-0c7146d

nf-core/bwa/sampe @ 0.0.0-0c7146d

Convert paired-end bwa SA coordinate files to SAM format

bwa aln short-read align reference fasta map sam bam

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Convert paired-end bwa SA coordinate files to SAM format

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

include { BWA_SAMPE } from 'nf-core/bwa/sampe'

MIT License

Process

`Name`	`BWA_SAMPE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test', single_end:false ]
`reads` file	FASTQ files specified alongside meta in input channel. `*.{fastq,fq}.gz`
`sai` file	SAI file specified alongside meta and reads in input channel. `*.sai`

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`index` directory	Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX `bwa/`

Output 3 channels

#1 bam tuple

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

#2 versions_bwa tuple

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

#3 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
bwa	BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.	http://bio-bwa.sourceforge.net/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:49:53 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbwa%2Fsampe/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bwa/sampe/blobs/sha256:19166b78f0dcd13036cbb3ed4556d68c5046a3bbbff42838d97cd534f0ed8fbd
Size	3.0 KB
Checksum	sha256:19166b78f0dcd13036cbb3ed4556d68c5046a3bbbff42838d97cd534f0ed8fbd
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:08:07 (UTC)		3	3.0 KB
0.0.0-0c7146d	08 Apr 2026 18:49:53 (UTC)		3	3.0 KB