nf-core/regtools/junctionsextract @ 0.0.0-0c7146d
Summary
Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
Get started
Add the following snippet to your workflow script to include this module.
include { REGTOOLS_JUNCTIONSEXTRACT } from 'nf-core/regtools/junctionsextract'
License
MIT License
Process
Name
|
REGTOOLS_JUNCTIONSEXTRACT |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
Sorted BAM file *.{bam}
|
bai
file
|
Index to sorted BAM file *.{bai}
|
strand_specificity
string
|
Strand specificity of the RNA-seq library preparation. Options are 'XS', use XS tags provided by aligner; 'RF', first-strand; 'FR', second-strand. |
|---|
Output
2 channels
#1
junc
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.junc
file
|
BED12 file containing exon-exon "regtools_junctionsextract" *.{junc}
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| regtools | RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. | https://regtools.readthedocs.io/en/latest/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:30:30 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fregtools%2Fjunctionsextract/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/regtools/junctionsextract/blobs/sha256:d63c3080c2b76585c78bf233f0474fb6b9ce1ded46d5f783f20c2e0b0f846405 |
| Size | 2.7 KB |
| Checksum | sha256:d63c3080c2b76585c78bf233f0474fb6b9ce1ded46d5f783f20c2e0b0f846405 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:40:37 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:30:30 (UTC) | 3 | 2.7 KB |