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Sydney-Informatics-Hub / ONT-bacpac-nf

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Consensus assembly: trycycler #10

Open georgiesamaha opened 2 weeks ago

georgiesamaha commented 2 weeks ago

Given trycycler is designed to be run manually, nextflowing it has been a bit tricky. We need to ensure all newly generated files are captured in specified output directories. Trycycler just adds files for each step to the same input directory. This breaks nextflow's rules re: reproducibility. To resolve, we have to rewrite processes to move outputs to a new directory that can be cached and picked up as input for future processes. All custom python scripts written to automate the manual steps must take this into consideration.

georgiesamaha commented 1 week ago

Trycycler also prints info to stdout, to capture this should use optional: true for outputs.