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

val(meta)

Outputs

Nextflow interface

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