# RUN_TRF

This process runs the TRF (Tandem Repeats Finder) tool to identify
tandem repeats in a genome file.
It uses the run_trf script to perform the analysis and generates a
GTF file containing the identified tandem repeats.
The output GTF file is saved in the "trf" directory under the output
directory for the given GCA accession.
The process also generates a versions.yml file containing the version
of TRF used.

## Process Details

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

## Inputs

### Nextflow interface

```nextflow
val(meta)
```

## Outputs

### Nextflow interface

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

## Implementation Summary

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

## Source

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