Nextflow Registry | nf-core/picard/collectwgsmetrics@0.0.0-0c7146d

nf-core/picard/collectwgsmetrics @ 0.0.0-0c7146d

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

alignment metrics statistics quality bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:02:37 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectwgsmetrics/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/collectwgsmetrics/blobs/sha256:98635e49b0c5c5413e58dd85573adcef6d8f5c38e4a300517b5ba45b94cafda3
Size	3.1 KB
Checksum	sha256:98635e49b0c5c5413e58dd85573adcef6d8f5c38e4a300517b5ba45b94cafda3
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:02:37 (UTC)		1	3.1 KB	-