Nextflow Registry | nf-core/samtools/splitheader@0.0.0-6c4ed3a

nf-core/samtools/splitheader @ 0.0.0-6c4ed3a

Extract header lines from a SAM/BAM/CRAM file into separate files depending on type

view bam sam cram readgroup program sequence header

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @matthdsm @prototaxites

Maintainers: @matthdsm @prototaxites

Extract header lines from a SAM/BAM/CRAM file into separate files depending on type

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

include { SAMTOOLS_SPLITHEADER } from 'nf-core/samtools/splitheader'

MIT License

Process

`Name`	`SAMTOOLS_SPLITHEADER`

Input 1 channel

#1 tuple

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

Output 4 channels

#1 programs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_programs.txt` file	Text file containing program (@PG) lines from SAM header

#2 readgroup tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_readgroups.txt` file	Text file containing read group (@RG) lines from SAM header

#3 sequences tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_sequences.txt` file	Text file containing sequence (@SQ) lines from SAM header

#4 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` string	The command used to generate the version of the tool

Tool	Description	Homepage
samtools	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:43:27 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fsplitheader/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/splitheader/blobs/sha256:df39cd718eb169635b75cceb650877764d296bb420394ea21fd5db00a8d85706
Size	3.0 KB
Checksum	sha256:df39cd718eb169635b75cceb650877764d296bb420394ea21fd5db00a8d85706
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:27 (UTC)		3	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:34:13 (UTC)		2	3.0 KB