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

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

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

merge convert readwriter sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file.

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

include { SENTIEON_READWRITER } from 'nf-core/sentieon/readwriter'

MIT License

Process

`Name`	`SENTIEON_READWRITER`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file. `*.{bam,cram}`
`index` file	BAI/CRAI file. `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`fasta` file	Genome fasta file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`fai` file	The index of the FASTA reference. `*.fai`

Output 4 channels

#1 index tuple

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

#2 output tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`${prefix}` file	BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = .bam", CRAM "ext.prefix = .cram". Defaults to cram `*.{bam,cram}`

#3 output_index tuple

`meta` map	Groovy Map containing reference information. e.g. [ id:'test', single_end:false ]
`${prefix}` file	BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = .bam", CRAM "ext.prefix = .cram". Defaults to cram `*.{bam,cram}`
`${prefix}.${index}` file	BAM/CRAM index file `*.{bai,crai}`

#4 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 15:44:06 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Freadwriter/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/readwriter/blobs/sha256:158ad043a61216d74956b00fa1ad1e27f24b2b6ea70d2e43bb7a07d388710498
Size	3.8 KB
Checksum	sha256:158ad043a61216d74956b00fa1ad1e27f24b2b6ea70d2e43bb7a07d388710498
Downloads	2

Version	Date	Status	Downloads	Size