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

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

Collect multiple metrics from a BAM file

alignment metrics statistics insert quality bam

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:35:56 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectmultiplemetrics/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/collectmultiplemetrics/blobs/sha256:b760514010846e0653f0dfcfa90736e5be3307d4a6736bf563fc38c4d2e2dffb
Size	3.3 KB
Checksum	sha256:b760514010846e0653f0dfcfa90736e5be3307d4a6736bf563fc38c4d2e2dffb
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:35:56 (UTC)		3	3.3 KB
0.0.0-0c7146d	08 Apr 2026 19:25:30 (UTC)		2	3.3 KB