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

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

Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.

alignment metrics statistics quality bam

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @drpatelh @flowuenne @lassefolkersen @ramprasadn

Maintainers: @drpatelh @flowuenne @lassefolkersen @ramprasadn

Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.

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

include { PICARD_COLLECTWGSMETRICS } from 'nf-core/picard/collectwgsmetrics'

MIT License

Process

`Name`	`PICARD_COLLECTWGSMETRICS`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Aligned reads file `*.{bam, cram}`
`bai` file	(Optional) Aligned reads file index `*.{bai,crai}`

#2 tuple

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

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Genome fasta file index `*.{fai}`

`intervallist` file	Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.

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 CollectWgsMetrics --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/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:36:00 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectwgsmetrics/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/collectwgsmetrics/blobs/sha256:c4bf0ad2f36491ec05c2d403ae2ccafb7dca446e3444d277a701dc9a2dabc0de
Size	3.1 KB
Checksum	sha256:c4bf0ad2f36491ec05c2d403ae2ccafb7dca446e3444d277a701dc9a2dabc0de
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:36:00 (UTC)		3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:25:36 (UTC)		3	3.1 KB