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!

Image

[bdvorsky]

You can edit main.nf configuration file to use the URL provided, edit this file on your machine running the pipeline: ~/.nextflow/assets/nf-core/rnafusion/modules/local/hgnc/main.nf

[dhlee3342]

@bdvorsky @madinolfi92 Thank you!