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

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

Collects whole genome quality metrics from a bam file

metrics bam sentieon

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Collects whole genome quality metrics from a bam file

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

include { SENTIEON_WGSMETRICS } from 'nf-core/sentieon/wgsmetrics'

MIT License

Process

`Name`	`SENTIEON_WGSMETRICS`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	Index of th sorted BAM/CRAM/SAM file `*.{bai,crai,sai}`

#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	Index of the genome fasta file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. `[ id:'test' ]`
`intervals_list` file	intervals

Output 2 channels

#1 wgs_metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.txt` file	File containing the information about mean base quality score for each sequencing cycle `*.txt`

#2 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 19:12:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fwgsmetrics/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sentieon/wgsmetrics/blobs/sha256:df7b6c61fa8bcc29837488da862a9a025a79b7d29d1c83bcdfe5fdc064be580c
Size	3.4 KB
Checksum	sha256:df7b6c61fa8bcc29837488da862a9a025a79b7d29d1c83bcdfe5fdc064be580c
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:12:25 (UTC)		1	3.4 KB	-