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

val(meta)

Outputs

Nextflow interface

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