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

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

Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads

sample bam sam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @bwlang

Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads

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

include { PICARD_POSITIONBASEDDOWNSAMPLESAM } from 'nf-core/picard/positionbaseddownsamplesam'

MIT License

Process

`Name`	`PICARD_POSITIONBASEDDOWNSAMPLESAM`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	BAM file `*.{bam,cram,sam}`
`fraction` float	Fraction of reads to downsample to

Output 4 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`.ds.bai` file	An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag `*.{bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`.ds.bam` file	A downsampled BAM file `*.{bam}`

#3 num_reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`ACTUAL_NUM_READS` integer	The actual number of downsampled reads

#4 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard PositionBasedDownsampleSam --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 15:36:14 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fpositionbaseddownsamplesam/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/positionbaseddownsamplesam/blobs/sha256:8e012bab06aca85b0a14298a3062524e721f7d17bb30e0ed8590bdbf117e86fb
Size	3.0 KB
Checksum	sha256:8e012bab06aca85b0a14298a3062524e721f7d17bb30e0ed8590bdbf117e86fb
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:36:14 (UTC)		3	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:25:57 (UTC)		3	3.0 KB