HGNC dataset download fails

[mialaalv]

Description of the bug

Download of the HGNC dataset (hgnc_complete_set.txt) fails because it is no longer available at the location the pipeline is trying to fetch it from (https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt).

All HGNC download files including the archive files are now in a publicly accessible Google Storage Bucket. The new link can be found at https://www.genenames.org/download/statistics-and-files/

I am creating a pull request with the modified URL.

Command used and terminal output

Caused by:
Process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) terminated with an error exit status (8)

Command executed:

wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD":
wget: $(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml)
END_VERSIONS

Command exit status:
8

Command output:
(empty)

Command error:
--2024-10-30 13:11:24-- https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
Resolving ftp.ebi.ac.uk... 193.62.193.165
Connecting to ftp.ebi.ac.uk|193.62.193.165|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2024-10-30 13:11:24 ERROR 404: Not Found.

Relevant files

No response

System information

No response

[madinolfi92]

I have the same problem. I downloaded the file from this url: https://ftp.ebi.ac.uk/pub/databases/genenames/out_of_date_hgnc/tsv/hgnc_complete_set.txt
and I created a new folder named hgnc to reference_genomes folder. I've also specified this path on the config file but still have the same problem.

Marta!

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