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@ewels mentioned that users like to modify this genomes config. In that case, it should be refactored into an index file (e.g. JSON, YAML). Then you can load it in the config, although it still might be easier to have a param for the file name (e.g. params.igenomes_index) and load it in the pipeline code:
Suggestion is to use a ternary expression, which should work:
// Load igenomes.config if required
includeConfig !params.igenomes_ignore ?'conf/igenomes.config':'conf/igenomes_ignored.config'
Where a new igenomes_ignored.config file would simply contain:
params.genomes = [:]
Can maybe think of more elegant syntax, but that's the gist of it.
Regarding (2) in the longer term - it'd be nice to rewrite how all of the iGenomes configuration works. This will break how existing user's config files work, but I think it's ok if we're overhauling the entire references system anyway. So hopefully we can incorporate this syntax change along with the new references back end.
The
params.genomes
is a map that is conditionally included, which is a very clever hack that will not be supported by the new config parser 😅Instead, I suggest refactoring the
igenomes.config
into a function that returns a giant map:You can then include this function into your workflow and use it however you want:
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