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

val(meta)

Outputs

Nextflow interface

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