nf-core/gatk4/mergebamalignment @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:42:42 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fmergebamalignment/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/mergebamalignment/blobs/sha256:59eee17fe38c3139d3231cd7022f0afd449be6d2118f0cc1e2e79d7cab0db814 |
| Size | 2.8 KB |
| Checksum | sha256:59eee17fe38c3139d3231cd7022f0afd449be6d2118f0cc1e2e79d7cab0db814 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:42:42 (UTC) | 1 | 2.8 KB | - |