nf-core/gatk4/filterintervals @ 0.0.0-0c7146d
Summary
Filters intervals based on annotations and/or count statistics.
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_FILTERINTERVALS } from 'nf-core/gatk4/filterintervals'
License
MIT License
Process
Name
|
GATK4_FILTERINTERVALS |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing reference information e.g. [ id:'test' ] |
|---|---|
intervals
file
|
Processed interval list file (processed_intervals.interval_list) *.interval_list
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
read_counts
file
|
Read counts input file *.{tsv, hdf5}
|
#3
tuple
meta3
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
annotated_intervals
file
|
Annotated intervals TSV file (annotated_intervals.tsv). *.tsv
|
Output
2 channels
#1
interval_list
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.interval_list
file
|
Filtered interval list file *.interval_list
|
#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 | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:03:09 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Ffilterintervals/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/filterintervals/blobs/sha256:dc816a29d41797e9957706e23efcf01f407bc7ec15a05e8a6a9818881d530d2e |
| Size | 2.9 KB |
| Checksum | sha256:dc816a29d41797e9957706e23efcf01f407bc7ec15a05e8a6a9818881d530d2e |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:18:47 (UTC) | 4 | 2.9 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:03:09 (UTC) | 3 | 2.9 KB |