Nextflow Registry | nf-core/rseqc/splitbam@0.0.0-6c4ed3a

nf-core/rseqc/splitbam @ 0.0.0-6c4ed3a

Split BAM file based on gene list in BED format

bam split rnaseq quality control

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @rhassaine

Maintainers: @rhassaine

Split BAM file based on gene list in BED format

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

include { RSEQC_SPLITBAM } from 'nf-core/rseqc/splitbam'

MIT License

Process

`Name`	`RSEQC_SPLITBAM`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Sorted BAM file `*.{bam}`
`bai` file	BAM index file `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'reference' ]`
`bed` file	Gene list in BED format to split the BAM by `*.{bed}`

Output 4 channels

#1 ex_bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.ex.bam` file	BAM file containing reads that did not map to the gene list `*.ex.bam`

#2 in_bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.in.bam` file	BAM file containing reads that mapped to the gene list `*.in.bam`

#3 junk_bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.junk.bam` file	BAM file containing QC failed or unmapped reads `*.junk.bam`

#4 versions_rseqc tuple

`${task.process}` string	The process the versions were collected from
`rseqc` string	The tool name
`split_bam.py --version \| sed "s/split_bam.py //"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
rseqc	RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.	http://rseqc.sourceforge.net/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:41:20 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Frseqc%2Fsplitbam/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/rseqc/splitbam/blobs/sha256:bc14b67b63ace365a1eb5275f40467ba148f77737e22b181f6dd82b6591cc38f
Size	2.7 KB
Checksum	sha256:bc14b67b63ace365a1eb5275f40467ba148f77737e22b181f6dd82b6591cc38f
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:41:20 (UTC)		4	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:32:17 (UTC)		4	2.7 KB