When all samples have only exclusive user-defined references. the pipeline breaks

nf-core / pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

https://nf-co.re/pathogensurveillance

MIT License

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When all samples have only exclusive user-defined references. the pipeline breaks #101

Closed zachary-foster closed 3 weeks ago

zachary-foster commented 1 month ago

This can be fixed by either changing the channels to not run PICK_ASSEMBLIES when in this case or changing PICK_ASSEMBLIES to take into account user-defined references. The first option results in fewer tasks being run, but has more complicated channel code.

zachary-foster commented 3 weeks ago

This has been fixed