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maxplanck-ie / nanoporeReads_dataTransfer

A pipeline to transfer the Nanopore reads to end users

MIT License

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Develop #117

Closed thomasmanke closed 1 year ago

thomasmanke commented 1 year ago

This is a rebased develop with main from #107
Key additions are:

multiqc
kraken2
storage report
porechop for adapter detection and trimming
dorado as optional basecaller (model choice still needs improvements)
GPU resource query before basecalling
new command line controls for source directory (only a single directory is now tracked for new flowcells)
new command line control for (organism and protocol) - side tracks parkour query

thomasmanke commented 1 year ago

I would change to 2.0.0 only until after dorado has become default. at the moment it is just an option. But dorado will require more testing and multiplexing capabilities.