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

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

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: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:12:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Freadwriter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sentieon/readwriter/blobs/sha256:98c8a1fab0835ad35fd89559e33951129b64000c35f5947af612beca0c9f4302
Size	3.8 KB
Checksum	sha256:98c8a1fab0835ad35fd89559e33951129b64000c35f5947af612beca0c9f4302
Downloads	1

Version	Date	Status	Downloads	Size	Diff