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

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

Splits a SAM/BAM/CRAM file to multiple files. This tool splits the input query-grouped SAM/BAM/CRAM file into multiple files while maintaining the sort order. This can be used to split a large unmapped input in order to parallelize alignment.

split parallel bam subset downsample sam cram

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @Y-Pei

Maintainers: @Y-Pei

Summary

Get started

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

include { PICARD_SPLITSAMBYNUMBEROFREADS } from 'nf-core/picard/splitsambynumberofreads'

License

MIT License

Process

`Name`	`PICARD_SPLITSAMBYNUMBEROFREADS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`input` file	BAM/SAM/CRAM file `*.{bam,sam,cram}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Reference fasta (optional - only required for CRAM input) `*.{fasta,fa}`
`fai` file	FAI file (optional - only required for CRAM input) `*.{fai}`

`split_to_N_reads` integer	Split to have approximately N reads per output file, e.g. `4000000`. The actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1). Incompatible with `split_to_N_files`

`split_to_N_files` integer	Split to N files, e.g. `3`. `Incompatible with split_to_N_files`

`arguments_file` file	optional Picard arguments file `*.{txt,list,args,arguments}`

Output 2 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`picardsplit/*.{bam,sam,cram}` file	Split BAM files `*.{bam,sam,cram}`

#2 versions_picard tuple

`${task.process}` string	The process the versions were collected from
`picard` string	The tool name
`picard SplitSamByNumberOfReads --version 2>&1 \| sed -n 's/.*Version://p'` string	The command used to generate the version of the tool

Tool	Description	Homepage
picard	Splits a SAM or BAM file to multiple BAMs by number of reads.	https://gatk.broadinstitute.org/hc/en-us/articles/360037064232-SplitSamByNumberOfReads-Picard

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:03:08 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fsplitsambynumberofreads/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/picard/splitsambynumberofreads/blobs/sha256:87b5a1043c0204a5a5621d8e193d5e320469f3dbbb0e7ffaa9fdc3e076456a8e
Size	4.0 KB
Checksum	sha256:87b5a1043c0204a5a5621d8e193d5e320469f3dbbb0e7ffaa9fdc3e076456a8e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:03:08 (UTC)		1	4.0 KB	-