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SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
68 stars 5 forks source link

Hook subsample_bam to be usable from manifest #23

Closed SamStudio8 closed 4 years ago

SamStudio8 commented 4 years ago

very exciting this has graduated from a potential enhancement to something that is broken, good job me

SamStudio8 commented 4 years ago

the first stage of the iterative polishing with subsampling works great and then we seem to end up in a strange feedback loop where we create the unsampled sam to try to polish again

SamStudio8 commented 4 years ago

i have attempted to fix this by forcing the input file to the polish_racon rule to be chosen by the setting of the depth wildcard (i dont really know why that would work which makes me think that it probably wont)

SamStudio8 commented 4 years ago

I think this works now, although the implementation is a bit grim

SamStudio8 commented 4 years ago

The main issue here was an attempt to be clever and save one BAM generation when repolishing.

SamStudio8 commented 4 years ago

Added by 37186e2e80ce16d4e4e34521d40279a76455674e Not sure how I feel about the implementation if I'm being honest