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SamStudio8 / reticulatus

A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
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Update and pin dependencies #55

Open SamStudio8 opened 2 years ago

SamStudio8 commented 2 years ago

Struggled to build the base env in some cases with medaka specified so I've put it in a conda jail that is only loaded if config.cuda is set to False (so we won't interfere with the Singularity container in the case of using --use-conda --use-singularity). Pinned the rest of the deps to more recent stable versions and tested this works with the classic Zymo dataset.

SamStudio8 commented 2 years ago

Checked rmdup and subset-N