Dorado basecalling workflow enhancements

[fraser-combe]

🆒

📌 Explain the Request

Propose enhancing the Dorado workflow with the following new features:

• Add a --notrim Option in Dorado demux task: Allow users to retain reads with barcodes untrimmed, which can be useful for troubleshooting. For instance, users can inspect untrimmed reads in the "unclassified" folder when data issues arise, such as mis-binned reads.

• Expose Custom Primer Trimming Options: Enable users to specify a custom set of primers for PCR primer trimming during the demultiplexing step. This will be achieved by integrating Dorado's --primer-sequences option, which accepts a FASTA file containing custom primer sequences. Note that using this option overrides the built-in primer sequences in Dorado.

Custom Primer Trimming Documentation from Dorado GitHub

Docker image could also be updated to Dorado 0.9.0 there is currently a PR for this on Staph-B

[AndrewLangvt]

@fraser-combe this work is being implemented in #659, correct?

[fraser-combe]

Yes ill update the PR once I complete it to refer to this issue