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

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: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @Y-Pei
Maintainers: @Y-Pei

Summary

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.

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 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:36:21 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fsplitsambynumberofreads/0.0.0-6c4ed3a/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/splitsambynumberofreads/blobs/sha256:4062f25150a805462c623975c8e0c02b246a484e54fb4112dcd7300fdc5547c5
Size 4.0 KB
Checksum sha256:4062f25150a805462c623975c8e0c02b246a484e54fb4112dcd7300fdc5547c5
Downloads 4
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:36:21 (UTC) 4 4.0 KB
0.0.0-3fc6d40 22 Apr 2026 15:25:42 (UTC) 3 4.1 KB
0.0.0-0c7146d 08 Apr 2026 19:26:07 (UTC) 3 4.0 KB