nf-core/samtools/reheader @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:10:27 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Freheader/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/samtools/reheader/blobs/sha256:8cf5e6d19171f2f29bad026b63585e98f20073034345e335eac0afaff9ca1ecf |
| Size | 2.8 KB |
| Checksum | sha256:8cf5e6d19171f2f29bad026b63585e98f20073034345e335eac0afaff9ca1ecf |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:27 (UTC) | 1 | 2.8 KB | - |