using ensemblgenomes for non-vertebrate references

[RvV1979]

Hi Johannes,
I am trying to implement the https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling workflow for non-vertebrate (plant) genomes that are available through ensemblgenomes.org. However, the https://github.com/snakemake/snakemake-wrappers/tree/master/bio/reference wrappers use only the canonical ensembl ftp site.

Is it possible to use these wrappers for ensemblgenomes ?

Thanks

[fgvieira]

The wrapper currently uses the URL ftp://ftp.ensembl.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}.

For ensembl genomes, would it be enough to change it to ftp://ftp.{source}.org/pub/{branch}release-{release}/fasta/{species}/{datatype}/{species_cap}.{spec}.{suffix}?

Can you provide an example snakemake rule for testing?

[fgvieira]

I believe this has been fixed on #546.
Can you double check?

[github-actions]

This issue was marked as stale because it has been open for 6 months with no activity.