nf-core/samtools/reheader @ 0.0.0-6c4ed3a
Summary
Replace the header in the bam file with the header generated by the command. This command is much faster than replacing the header with a BAM→SAM→BAM conversion.
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_REHEADER } from 'nf-core/samtools/reheader'
License
MIT License
Process
Name
|
SAMTOOLS_REHEADER |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
BAM/CRAM file to be reheaded *.{bam,cram}
|
bai
file
|
BAM/CRAM index file to be reheaded *.{bai,crai,csi}
|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Reheaded BAM/CRAM file *.{bam,cram}
|
#2
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed '1!d;s/.* //'
eval
|
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 15:43:22 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Freheader/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/reheader/blobs/sha256:10e21a6eee9c8f7596d52e1c67cd0fabd3f777908f1b1d361ae53152ff833722 |
| Size | 2.8 KB |
| Checksum | sha256:10e21a6eee9c8f7596d52e1c67cd0fabd3f777908f1b1d361ae53152ff833722 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:43:22 (UTC) | 2 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:34:05 (UTC) | 2 | 2.8 KB |