CHECK_AND_DOWNLOAD_RMLIBRARY

This process checks if a RepeatModeler library file exists at the given URL. If the file exists, it downloads the file and saves it with the name “. repeatmodeler.fa”. If the file does not exist, it outputs an error message and exits with a non-zero status.

Process Details

Property	Value
Process	CHECK_AND_DOWNLOAD_RMLIBRARY
Label	'default'
Tag	$meta.gca
Publish directory	"${params.outdir}/${meta.gca}/rm_library", mode: 'copy'

Inputs

Name	Description
meta	Genome metadata map
url	RepeatModeler library URL

Nextflow interface

tuple val(url), val(meta)

Outputs

Name	Description
meta	Genome metadata map
fasta_file	RepeatModeler library file

Nextflow interface

tuple val(meta), path("*.fa"), emit: repeatmodeler_library_out
path "versions.yml", emit: versions_file

Implementation Summary

• Download external resources

• Generate software version report

Source

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