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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Run pangolin on concatinated consensus file #6

Closed sylvinite closed 3 years ago

sylvinite commented 3 years ago

What needs to be done: Currently pangolin is ran on individual consensus files. Pangolin needs to be ran on a concatinated consensus file.

Suggestions on how to get it done: Change the input stream in the nextflow script

What are the arguments for getting it done: Building a report function afterwards kind of requires it. It is cleaner to do it like this than to build it into the report itself

Task is considered finished when: There's a single pangolin file for a batch project that encompasses all samples

pbiology commented 3 years ago

In terms of scale, perhaps it would be better to keep the pangolin jobs separate, and then concatenate all results in the final collate step of the pipeline?

sylvinite commented 3 years ago

Sounds good