Another ensemble_vep question. I am using it without a prebuild cache but with just a gff file. Is it possible to do that with the ensemble_vep module? I do not see a way to not use the --cache option. Is that by design or was it simply not needed till now?

@Fabian Friedrich, you could just add your options to conf/modules.config file. These are then passed as $args into the module Under process, simply add:

withName: 'ENSEMBLVEP_VEP' {
   ext.args = 'list your options to pass to module'
   publishDir = ...
}

Yes, but the actual vep command sets the cache option in the module, which then require a cache. So I am using a local copy of that module where I have deleted all the params I am not using (

--cache --cache_version --dir_cache

). But I am thinking of adding these options to the official module if somebody else needs it, as I would say that my workaround is not the prettiest.

vep \\
        -i ${vcf} \\
        -o ${prefix}.${file_extension}.gz \\
        ${args} \\
        ${compress_cmd} \\
        ${reference} \\
        --assembly ${genome} \\
        --species ${species} \\
        --cache \\
        --cache_version ${cache_version} \\
        --dir_cache ${dir_cache} \\
        --fork ${task.cpus}