# RUN_RED

This process runs the Red to identify repetitive regions in a genome file.
It uses the Red tool to perform the analysis and generates a GTF file
containing the identified repetitive regions. The output GTF file is
saved in the "red" directory under the output directory for the given
GCA accession. The process also generates a versions.yml
file containing the version of Red used.

## Process Details

| Property | Value |
|----------|-------|
| Process | `RUN_RED` |
| Label | `python` |
| Tag | `${meta.gca}:genome` |
| Publish directory | `"${params.outdir}/${meta.gca}/red/", pattern: "**/*.gtf", mode: "copy"` |

## Inputs

### Nextflow interface

```nextflow
val(meta)
```

## Outputs

### Nextflow interface

```nextflow
tuple val(meta), path("*.gtf"), emit: red_out
path "versions.yml", emit: versions_file
```

## Implementation Summary

- Execute Run Red
- Rename output files
- Generate software version report

## Source

`/home/runner/work/ensembl-genes-nf/ensembl-genes-nf/pipelines/repeat/modules/run_red.nf`