sanger-tol/ensemblgenedownload is a pipeline that downloads gene annotations from Ensembl into a Tree of Life directory structure.

The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, geneset methods and geneset versions. The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file. All files are compressed with bgzip, and indexed with samtools faidx or tabix.

Steps involved:

  • Download from Ensembl the GFF3 file, and the sequences of the genes in Fasta format.
  • Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict.
  • Compress and index the GFF3 file with bgzip and tabix.

[!WARNING] Only the Rapid Release site is currently supported, not the other Ensembl sites.


Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

The easiest is to provide the exact species name and versions of the assembly and annotations like this:

nextflow run sanger-tol/ensemblgenedownload --ensembl_species_name Noctua_fimbriata --assembly_accession GCA_905163415.1 --annotation_method braker --geneset_version 2022_03

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

The pipeline also supports bulk downloads through a sample-sheet. More information about this mode on our pipeline website.


sanger-tol/ensemblgenedownload was originally written by Matthieu Muffato.

We thank the following people for their assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #pipelines channel. Please create an issue on GitHub if you are not on the Sanger slack channel.


If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: 10.5281/zenodo.7155206

An extensive list of references for the tools used by the pipeline can be found in the file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

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Read how to configure the Seqera Platform CLI here.

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