New version of the Viral Discovery pipeline from B. Andersson's lab @ Karolinska Institutet. Implemented using Nextflow
The pipeline is split in two parts:
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Preprocessing: Does QC on the sequences, removes adapters (including SISPA adapters from our viral discovery protocol) and removes human by mapping to a reference.
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Discovery: Search the sequences with as much stuff as we can. Hope we can develop a way of nicely summarizing the results so that the information is easy to use and hopefully discover new stuff !
In theory, it should be as simple (lol) as installing all the dependencies, and creating a suitable config file with the paths to them.
TODO: In practice, automate this in some way! maybe conda?
Check the docs/ folder!