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

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

Collect multiple metrics from a BAM file

alignment metrics statistics insert quality bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @drpatelh

Maintainers: @drpatelh

Collect multiple metrics from a BAM file

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

include { PICARD_COLLECTMULTIPLEMETRICS } from 'nf-core/picard/collectmultiplemetrics'

MIT License

Process

`Name`	`PICARD_COLLECTMULTIPLEMETRICS`

Input 3 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome']
`fasta` file	Genome fasta file

#3 tuple

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

Output 3 channels

#1 pdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pdf` file	PDF plots of metrics `*.{pdf}`

#2 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}`

#3 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard CollectMultipleMetrics --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 19:02:31 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectmultiplemetrics/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/collectmultiplemetrics/blobs/sha256:97b46fd12a2439a7ef6d743a9ed085c99d75985155c52642528cf545d35cb83a
Size	3.3 KB
Checksum	sha256:97b46fd12a2439a7ef6d743a9ed085c99d75985155c52642528cf545d35cb83a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:02:31 (UTC)		1	3.3 KB	-