RUN_REPEATMASKER

This process runs RepeatMasker on a given genome file using a specified RepeatModeler library. It uses the RepeatMasker tool to perform the analysis and generates GTF files containing the identified repetitive regions. The output GTF files are saved in the “repeatmasker” directory under the output directory for the given GCA accession. The process also generates a versions.yml file containing the version of RepeatMasker used.

Process Details

Property	Value
Process	`RUN_REPEATMASKER`
Label	`python`
Tag	`${meta.gca}:genome`
Publish directory	`"${params.outdir}/${meta.gca}/repeatmasker/", pattern: "repeatmasker_output/*.gtf", mode: "copy"`

Inputs

Nextflow interface

tuple val(meta), val(library_file)

Outputs

Nextflow interface

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

Implementation Summary

Execute Run Repeatmasker
Rename output files
Generate software version report

Source

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