Nextflow Registry | nf-core/picard/collecthsmetrics@0.0.0-6c4ed3a

nf-core/picard/collecthsmetrics @ 0.0.0-6c4ed3a

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

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @projectoriented @matthdsm

Maintainers: @projectoriented @matthdsm

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

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

include { PICARD_COLLECTHSMETRICS } from 'nf-core/picard/collecthsmetrics'

MIT License

Process

`Name`	`PICARD_COLLECTHSMETRICS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	An aligned BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	Optional aligned BAM/CRAM/SAM file index `*.{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:'genome' ]
`ref` file	A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input. `*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`ref_fai` file	Index of reference file. Only needed when reference is supplied. `*.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`ref_dict` file	Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied. `*.dict`

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`ref_gzi` file	Index of reference file. Only needed when gzipped reference is supplied. `*.gzi`

Output 2 channels

#1 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_metrics` file	Alignment metrics files generated by picard `*_{metrics}`

#2 versions_picard tuple

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

Tool	Description	Homepage
picard	A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.	https://broadinstitute.github.io/picard/

Checksum
Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:35:54 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollecthsmetrics/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/collecthsmetrics/blobs/sha256:d6349cd15975984ab5abf1f9cfb4f5fb24d90b88133d1f9c838282d6b6e1e8e6
Size	5.4 KB