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

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

Collects hybrid-selection (HS) metrics for a SAM or BAM file.

metrics bam sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @sppearce

Maintainers: @sppearce

Collects hybrid-selection (HS) metrics for a SAM or BAM file.

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

include { SENTIEON_HSMETRICS } from 'nf-core/sentieon/hsmetrics'

MIT License

Process

`Name`	`SENTIEON_HSMETRICS`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test']`
`bam` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	Index of the BAM/CRAM/SAM file `*.{bai,crai,sai}`
`bait_intervals` file	An interval file that contains the locations of the baits used. `*.{interval_list,bed,bed.gz}`
`target_intervals` file	An interval file that contains the locations of the targets. `*.{interval_list,bed,bed.gz}`

#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`

Output 2 channels

#1 metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.txt` file	Alignment metrics related to how many reads overlap the target/bait regions. `*.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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:44:04 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Fhsmetrics/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sentieon/hsmetrics/blobs/sha256:730e0db2055836dd67fd5c2f76c298d7a2bc2e8284f8dcc7654ef877fbe530fc
Size	4.0 KB
Checksum	sha256:730e0db2055836dd67fd5c2f76c298d7a2bc2e8284f8dcc7654ef877fbe530fc
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:44:04 (UTC)		4	4.0 KB
0.0.0-0c7146d	08 Apr 2026 19:35:57 (UTC)		3	4.0 KB