nf-core/gatk4/mergebamalignment @ 0.0.0-6c4ed3a
Summary
Merge unmapped with mapped BAM files
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_MERGEBAMALIGNMENT } from 'nf-core/gatk4/mergebamalignment'
License
MIT License
Process
Name
|
GATK4_MERGEBAMALIGNMENT |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test'] |
|---|---|
aligned
file
|
The aligned bam file *.{bam}
|
unmapped
file
|
The unmapped bam file *.{bam}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
The reference fasta file |
#3
tuple
meta3
map
|
Groovy Map containing reference information e.g. [ id:'genome' ] |
|---|---|
dict
file
|
GATK sequence dictionary |
Output
2 channels
#1
bam
tuple
meta
file
|
The merged bam file *.bam
|
|---|---|
*.bam
file
|
The merged bam file *.bam
|
#2
versions_gatk4
tuple
${task.process}
string
|
The name of the process |
|---|---|
gatk4
string
|
The name of the tool |
gatk --version | sed -n '/GATK.*v/s/.*v//p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gatk4 | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. | https://gatk.broadinstitute.org/hc/en-us |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:20:15 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fmergebamalignment/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/mergebamalignment/blobs/sha256:97e3a48fc8cc453ea9040f585dc0a718f5da99a1c6cc31fa2c92dcc55902ec6c |
| Size | 2.8 KB |
| Checksum | sha256:97e3a48fc8cc453ea9040f585dc0a718f5da99a1c6cc31fa2c92dcc55902ec6c |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:20:15 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:04:21 (UTC) | 4 | 2.8 KB |