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snakemake-workflows / dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
MIT License
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Revel download link does not work #169

Closed sci-kai closed 1 year ago

sci-kai commented 1 year ago

Hi, when running the pipeline, the revel download link does not work:

Error in rule download_revel:
    jobid: 73
    output: resources/revel_scores.zip
    log: logs/vep_plugins/download_revel.log (check log file(s) for error message)
    shell:
        curl https://rothsj06.u.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip -o resources/revel_scores.zip &> logs/vep_plugins/download_revel.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I currently downloaded the revel plugin through this link: https://zenodo.org/record/7072866/files/revel-v1.3_all_chromosomes.zip?download=1

Can you fix the link?

Best Kai

FelixMoelder commented 1 year ago

Thanks for reporting this. @johanneskoester It seems like the link is changing from time to time. Maybe we should allow to set it in the config file?

sci-kai commented 1 year ago

Fixed with #172 pull request