nf-core/gatk4/printsvevidence @ 0.0.0-6c4ed3a
Summary
WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.
Get started
Add the following snippet to your workflow script to include this module.
include { GATK4_PRINTSVEVIDENCE } from 'nf-core/gatk4/printsvevidence'
License
MIT License
Name
|
GATK4_PRINTSVEVIDENCE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
evidence_files
file
|
The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence. *.{pe,sr,baf,rd}.txt(.gz)
|
evidence_indices
file
|
The indices of the evidence files created by CollectSVEvidence *.{pe,sr,baf,rd}.txt(.gz).tbi
|
bed
file
|
An optional BED file *.bed
|
|---|
fasta
file
|
An optional reference FASTA file *.{fa,fasta}
|
|---|
fasta_fai
file
|
An optional reference FASTA file index *.fai
|
|---|
dict
file
|
The mandatory sequence dictionary file *.dict
|
|---|
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 |
printed_evidence
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt.gz
file
|
The output file containing the discordant read pairs or the soft clipped reads *.{pe,sr,baf,rd}.txt.gz
|
printed_evidence_index
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt.gz.tbi
file
|
The index file of the output compressed text file containing the discordant read pairs or the soft clipped reads *.{pe,sr,baf,rd}.txt.gz.tbi
|
| 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 15:20:26 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fprintsvevidence/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gatk4/printsvevidence/blobs/sha256:7ec6e3f0efbe60de6c6c9f13fbfb49001e4051f64b535595fcea7808d09295c4 |
| Size | 3.8 KB |
| Checksum | sha256:7ec6e3f0efbe60de6c6c9f13fbfb49001e4051f64b535595fcea7808d09295c4 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:20:26 (UTC) | 1 | 3.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:04:36 (UTC) | 1 | 3.8 KB |