FETCH_REPEAT_MODEL

This process fetches the RepeatModeler library file for a given GCA accession. If the file is available at the specified URL, it downloads the file and saves it with the name “.repeatmodeler.fa”. If the file is not available, it outputs a message indicating that the download was skipped and creates an empty file with the same name. The fetched library file is saved in the “library” directory under the output directory for the given GCA accession.

Process Details

Property	Value
Process	`FETCH_REPEAT_MODEL`
Label	`'fetch_file'`
Tag	`$meta.gca:repeatmodel`
Publish directory	`"${params.outdir}/${meta.gca}/library/", mode: 'copy'`

Inputs

Nextflow interface

val(meta)

Outputs

Nextflow interface

tuple val(meta), path("${meta.gca}.repeatmodeler.fa"), emit: rep_library_file_output
path "versions.yml", emit: versions_file

Implementation Summary

Generate software version report
Download external resources

Source

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