# GENERATE_REPEATMODELER_LIBRARY

This process runs RepeatModeler on a given genome file to generate a RepeatModeler library.
It uses the BuildDatabase tool to create a database from the genome file and then runs
RepeatModeler with the specified engine and number of threads.
The output files are renamed to include the GCA accession in their names
and are saved in the "library" directory under the output directory for
the given GCA accession. The process also generates a versions.yml file
containing the version of RepeatModeler used.

## Process Details

| Property | Value |
|----------|-------|
| Process | `GENERATE_REPEATMODELER_LIBRARY` |
| Label | `'repeatmodeler'` |
| Tag | `$meta.gca:run_repeatmodeler` |
| Publish directory | `"${params.outdir}/${meta.gca}/library", mode: 'copy'` |

## Inputs

### Nextflow interface

```nextflow
val(meta)
```

## Outputs

### Nextflow interface

```nextflow
tuple val(meta), path("*repeatmodeler.fa"), path("*families.stk.gz"), path("*rmod.log"), emit: repeatmodeler_library_out
path "versions.yml", emit: versions_file
```

## Implementation Summary

- Rename output files
- Generate software version report

## Source

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