dorado_trimming feedback from testing

[TomHarrop]

@AnnaSyme I'm tracking changes for the dorado read trimmer here, let me know if there's anything else!

• Don't allow custom primers with --no-trim-primers

[AnnaSyme]

thanks @TomHarrop !

[AnnaSyme]

@TomHarrop to convert the output bam file of trimmed reads to fastq, I'm using "samtoFastq", but it's giving me an error.
history: https://dev.gvl.org.au/u/annasyme/h/dorado
not sure if this is something to do with the dorado output itself, or something else. Edited to add: just saw on a different tool that Galaxy does not support bam files that are not coordinate sorted. Do you know if that's right.

[TomHarrop]

@AnnaSyme I've used Samtools fastx to get the reads out of the basecalling files. I think it should work for the trimming output too.

[AnnaSyme]

@TomHarrop that looks good, yes. Edited rest of this message as I got confused between adapter removal and error correction!